Loading Packages and Data From A2

if (!require("knitr", quietly = TRUE))
  install.packages("knitr")
if (!require("RSQLite", quietly = TRUE)){
  install.packages("RSQLite")
}

library(knitr)
library(RSQLite)
load("A3.RData")

The ranked gene list from A2 is shown below. There are multiple parameters that can be selected. We selected to use the up-regulated rank by logFC, to keep same with the original paper. Original data GSE_150392 can be downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150392

[1]

knitr::kable(MultipuleRank, caption = 'Table 1. Ranked Gene list by logFC Up-Regulated')
Table 1. Ranked Gene list by logFC Up-Regulated
Gene logFC logCPM F PValue FDR
PGAM2 -5.823109 5.602283 114.57596 0.0000032 0.0012769
KCNIP2 -5.719563 4.086743 160.76552 0.0000007 0.0007268
MYL2 -5.499684 10.723374 108.19050 0.0000040 0.0012869
FBXL22 -5.289779 3.678330 113.60661 0.0000033 0.0012869
ALAS2 -5.044219 5.316813 210.75460 0.0000002 0.0007000
METTL7B -4.984911 3.734938 68.29247 0.0000241 0.0024364
HHATL -4.724839 4.224531 108.70331 0.0000039 0.0012869
ACTA1 -4.549569 7.045206 63.09443 0.0000326 0.0027663
FXYD1 -4.430060 5.376322 55.46745 0.0000529 0.0032675
SPC25 -4.366327 2.902875 43.86371 0.0001256 0.0052210
FAM111B -4.336571 2.874277 102.56547 0.0000044 0.0012883
LINC02502 -4.298162 2.405372 24.32000 0.0009597 0.0161242
TNNC1 -4.285373 9.436908 94.52402 0.0000068 0.0014874
IRX4-AS1 -4.282455 2.134377 20.00454 0.0017844 0.0229872
COX6A2 -4.168300 2.086863 25.38949 0.0008339 0.0148626
PBK -4.114213 3.718915 170.56504 0.0000005 0.0007127
TCAP -4.067439 6.552621 80.76739 0.0000126 0.0017434
CENPM -4.064744 3.126273 42.12308 0.0001454 0.0056996
MSS51 -4.049343 3.683218 103.53421 0.0000047 0.0012904
TMSB15A -4.023837 3.743561 37.09184 0.0002289 0.0074975
TNMD -4.017588 5.303521 89.96110 0.0000083 0.0015101
MAOB -4.013483 2.448577 65.21380 0.0000287 0.0026349
S100A8 -3.987699 1.883211 20.61993 0.0016239 0.0217399
ADPRHL1 -3.938632 5.307378 158.94060 0.0000007 0.0007268
MYL7 -3.935387 12.710147 65.20630 0.0000287 0.0026349
ODAM -3.875695 1.766859 30.72430 0.0018866 0.0238249
CKMT2 -3.843017 6.214901 138.62454 0.0000013 0.0008940
CCDC34 -3.807975 5.223245 66.11307 0.0000273 0.0025570
TROAP -3.795809 2.443732 84.78398 0.0000090 0.0015377
FGF12 -3.795245 6.805036 156.87407 0.0000007 0.0007268
ACE2 -3.792261 3.553994 22.73039 0.0011935 0.0182253
MYL4 -3.789321 10.195632 76.73172 0.0000154 0.0019481
NME5 -3.772923 2.783836 48.77469 0.0000852 0.0041860
HSPB7 -3.772049 10.052815 166.34553 0.0000006 0.0007127
CPNE5 -3.696151 5.992740 171.99675 0.0000005 0.0007127
CORIN -3.695186 6.589812 61.16965 0.0000366 0.0028743
RAD51AP1 -3.668636 2.661695 104.40286 0.0000039 0.0012869
SUSD2 -3.664531 3.047584 46.43830 0.0001020 0.0046244
NAV2-AS2 -3.659570 5.527039 60.34002 0.0000386 0.0029093
TNNI1 -3.649594 10.687197 83.04644 0.0000113 0.0016217
GJD2 -3.648797 2.004456 64.36838 0.0005406 0.0116472
LDB3 -3.633489 7.996646 144.52753 0.0000010 0.0008348
GINS2 -3.632645 3.427047 75.81022 0.0000161 0.0019774
PCLAF -3.618731 3.518891 31.51488 0.0004036 0.0100969
MYLK-AS1 -3.614126 3.636269 25.19938 0.0008547 0.0150415
ACTC1 -3.599775 13.373242 95.08687 0.0000057 0.0014052
MIR133A1HG -3.586468 3.376682 55.81417 0.0000517 0.0032300
LINC01611 -3.581984 2.196025 20.81456 0.0015769 0.0214442
LDHD -3.576655 2.728602 102.45834 0.0000042 0.0012883
LINC01182 -3.561014 2.109034 21.69740 0.0013837 0.0199363
SLC35D3 -3.553160 1.849767 65.26468 0.0019145 0.0240364
CD36 -3.544471 5.422586 121.37468 0.0000022 0.0011591
MB -3.542870 7.055788 97.04714 0.0000061 0.0014197
MARCHF11 -3.530975 3.912894 59.83615 0.0000398 0.0029469
FABP3 -3.492141 9.278923 59.86107 0.0000397 0.0029469
TNNI3 -3.479622 9.576369 58.99188 0.0000420 0.0030190
C1QL1 -3.445765 4.228980 53.15605 0.0000620 0.0035473
MYH7 -3.415903 11.653417 21.54393 0.0014151 0.0202251
HSPB3 -3.409678 6.944682 64.26989 0.0000304 0.0026939
LMOD2 -3.403714 6.089989 142.83660 0.0000011 0.0008348
SMPX -3.395799 7.962930 59.92075 0.0000396 0.0029469
GPD1 -3.377976 2.085860 75.09594 0.0005304 0.0115514
DLGAP5 -3.375682 3.879891 72.90729 0.0000187 0.0021763
ATP6V1G2 -3.357918 2.813120 35.17433 0.0002758 0.0083139
AURKB -3.351708 3.019736 51.41282 0.0000702 0.0037726
CDKN3 -3.334427 3.629323 39.82371 0.0001778 0.0065217
CENPU -3.303800 4.258795 114.11012 0.0000027 0.0012769
TRIM54 -3.298866 3.697847 93.65253 0.0000064 0.0014424
FITM1 -3.291142 6.445232 45.38724 0.0001109 0.0048176
OIP5 -3.282617 2.587212 64.26485 0.0000292 0.0026381
FSD2 -3.274605 4.403858 46.69062 0.0001000 0.0045547
NDC80 -3.269491 3.617126 87.75540 0.0000086 0.0015265
CHCHD10 -3.261912 4.051329 37.10621 0.0002286 0.0074975
FAM133A -3.237091 1.828973 31.89990 0.0035706 0.0351559
DMAC1 -3.234254 5.058723 50.98336 0.0000724 0.0038494
KLHDC9 -3.218902 2.751979 39.92567 0.0001762 0.0065139
PPP1R1A -3.171572 5.119336 66.15034 0.0000272 0.0025570
LSMEM2 -3.164595 4.363786 59.04122 0.0000419 0.0030190
SPSB4 -3.155675 3.233936 56.20985 0.0000503 0.0031761
NUF2 -3.151356 2.999939 89.38433 0.0000073 0.0015101
TESC -3.150083 4.749327 76.28222 0.0000157 0.0019675
CALN1 -3.145096 4.329778 45.04932 0.0001140 0.0049161
PLCB2 -3.129927 3.219895 51.74126 0.0000685 0.0037557
AIF1L -3.108962 6.167169 83.38509 0.0000111 0.0016097
ITGB1BP2 -3.103756 5.368974 86.36585 0.0000097 0.0015449
PPP1R1C -3.100553 3.392007 44.24209 0.0001217 0.0051481
FGF13-AS1 -3.097264 1.849855 30.03096 0.0040713 0.0379895
SLC5A12 -3.096242 2.155342 42.05370 0.0006515 0.0129466
NPPA -3.091703 12.905503 43.44037 0.0001301 0.0053098
CDCA3 -3.086259 3.713057 43.92216 0.0001250 0.0052069
GABRA4 -3.068427 3.055071 56.75777 0.0000485 0.0031436
CAV3 -3.066379 3.136842 54.16213 0.0000578 0.0034176
KIF20A -3.066232 4.724288 37.42469 0.0002218 0.0073503
SELENOP -3.060758 6.162977 101.98209 0.0000045 0.0012883
CRYM -3.048275 3.285350 63.43901 0.0000319 0.0027505
DHFR -3.035134 4.171379 97.32632 0.0000052 0.0013682
BBOX1-AS1 -3.034916 1.824077 29.38297 0.0052955 0.0449764
ZWINT -3.030731 4.480563 108.41300 0.0000034 0.0012869
SPC24 -3.025167 2.311906 38.16759 0.0002206 0.0073354
COL9A1 -3.024658 2.758275 46.92348 0.0000982 0.0045464
PANCR -3.015240 1.815120 14.93628 0.0055620 0.0463645
NUDT7 -3.015061 3.352483 53.07165 0.0000624 0.0035579
C1orf105 -3.013779 4.009494 32.81289 0.0003512 0.0094029
HOPX -3.009609 7.911857 53.76810 0.0000594 0.0034598
TOP2A -3.004569 5.879015 28.96886 0.0005376 0.0116181
FRMD3 -2.990653 5.739911 93.15264 0.0000067 0.0014750
G0S2 -2.979050 7.268480 56.38213 0.0000498 0.0031761
LINC01405 -2.969873 2.961599 26.87404 0.0006912 0.0134324
AQP10 -2.967106 3.608513 79.67574 0.0000124 0.0017273
PTGES3L -2.953571 4.445324 71.78529 0.0000199 0.0022436
SGO1 -2.953492 2.308654 44.24394 0.0002917 0.0085806
NEIL3 -2.948272 2.142895 30.75930 0.0009914 0.0163900
HRC -2.948080 5.050080 67.43540 0.0000253 0.0025180
UBE2T -2.922022 5.089443 52.70717 0.0000640 0.0036260
RXRG -2.913305 2.757656 58.02664 0.0000435 0.0030255
NREP -2.911058 9.793089 100.85041 0.0000045 0.0012883
MCM5 -2.908502 4.683402 83.03824 0.0000108 0.0016057
C11orf52 -2.904686 1.917112 31.22355 0.0040481 0.0378087
CSRP3 -2.882775 10.273352 52.55780 0.0000647 0.0036353
LEFTY2 -2.880727 6.331081 85.03661 0.0000098 0.0015449
LGALS3 -2.871758 6.964936 44.40718 0.0001201 0.0051121
VSTM2L -2.866543 4.189090 83.29184 0.0000103 0.0015856
CRIP1 -2.865284 2.788855 15.70018 0.0036869 0.0358349
KIF2C -2.860460 3.511325 37.99659 0.0002102 0.0071578
ENPP5 -2.856968 2.969325 62.31754 0.0000331 0.0027908
NCAPH -2.854564 2.669372 48.09446 0.0000897 0.0043060
LINC01456 -2.832459 2.159370 22.93684 0.0011594 0.0178687
FMC1 -2.830633 3.939974 14.24424 0.0048637 0.0425396
HMGB2 -2.830279 6.353012 70.47858 0.0000213 0.0023028
IMMP1L -2.829254 3.758604 27.23721 0.0006610 0.0130629
EMC10 -2.824767 7.218908 53.96630 0.0000586 0.0034433
RAB9B -2.823723 5.225387 84.33594 0.0000098 0.0015449
TNNT2 -2.820532 11.602913 85.74207 0.0000086 0.0015265
ASF1B -2.817701 3.439544 58.59071 0.0000431 0.0030190
SLC38A3 -2.806756 2.273880 56.91351 0.0006085 0.0124300
SLC15A2 -2.804699 3.817950 18.75361 0.0021757 0.0260484
SRPK3 -2.800609 2.518381 55.37483 0.0000997 0.0045547
SMIM1 -2.796013 2.308004 20.64358 0.0016181 0.0217183
H4C3 -2.794520 6.630227 31.07645 0.0004235 0.0103480
CSPG5 -2.786076 3.521300 34.54088 0.0002939 0.0086206
MOG -2.766072 4.236609 84.58887 0.0000092 0.0015377
SH3BGR -2.764689 7.778034 64.79127 0.0000294 0.0026381
REC114 -2.761811 1.908698 38.33366 0.0057718 0.0472623
FPGT-TNNI3K -2.753526 4.400054 45.86065 0.0001068 0.0047481
EPN3 -2.749571 2.721405 37.55292 0.0002191 0.0073154
PIMREG -2.749342 3.111311 29.93996 0.0004808 0.0110608
NMRK2 -2.747681 3.532615 34.16588 0.0003053 0.0087842
TRDN -2.737878 7.398021 49.95256 0.0000781 0.0039752
POLE2 -2.734335 2.297587 44.12856 0.0006263 0.0126560
CDC45 -2.726066 2.708403 75.86047 0.0000294 0.0026381
DIRAS3 -2.722534 5.246650 76.62062 0.0000147 0.0019306
AMT -2.719618 4.128716 81.19617 0.0000109 0.0016057
SPX -2.708569 3.364626 45.78802 0.0001074 0.0047481
CEP55 -2.708550 3.253160 49.05146 0.0000835 0.0041158
CDCA8 -2.698342 2.891869 74.74704 0.0000149 0.0019306
PEBP4 -2.695043 2.159622 27.51015 0.0016200 0.0217289
HRH2 -2.694184 4.686904 80.59530 0.0000115 0.0016253
LINC00881 -2.692807 6.336775 48.43943 0.0000874 0.0042358
SORCS3 -2.687721 2.202008 16.34044 0.0032823 0.0334246
SMYD1 -2.687409 8.634806 28.36640 0.0005770 0.0120621
GPR22 -2.683250 5.043313 53.23310 0.0000617 0.0035385
SYNPO2L -2.672782 7.679458 109.86419 0.0000032 0.0012769
IGSF5 -2.672417 1.938644 22.12059 0.0058814 0.0477494
SPHKAP -2.668391 4.785341 15.14208 0.0040910 0.0380828
ANLN -2.662587 6.618821 17.22171 0.0028113 0.0304452
CAVIN3 -2.661827 4.205267 34.28699 0.0003016 0.0087394
CASQ2 -2.660241 7.989766 60.47205 0.0000382 0.0029093
PLAC1 -2.658369 2.116653 36.02356 0.0023151 0.0270255
MYZAP -2.654654 7.178472 60.03675 0.0000393 0.0029433
GPX3 -2.652738 7.094667 68.89002 0.0000232 0.0023965
SGCA -2.644098 4.754303 41.16441 0.0001579 0.0060764
DTL -2.641167 3.591869 30.23422 0.0004651 0.0109002
SLC27A6 -2.640879 6.575514 54.23099 0.0000575 0.0034118
PDE1A -2.636327 3.385269 23.96150 0.0010071 0.0165225
UBE2E1 -2.633303 4.594498 69.68775 0.0000218 0.0023298
TYRP1 -2.631008 2.466986 40.73282 0.0002766 0.0083233
MLIP -2.626909 7.348806 84.30360 0.0000092 0.0015377
TMEM71 -2.625232 4.413872 97.84239 0.0000051 0.0013501
C11orf71 -2.622072 3.166488 38.02702 0.0002096 0.0071578
NDUFB1 -2.617046 6.337492 30.04038 0.0004754 0.0110002
CASQ1 -2.614019 4.993688 68.94170 0.0000227 0.0023790
BIRC5 -2.603424 5.104400 93.38285 0.0000061 0.0014197
TMEM163 -2.592041 3.422335 50.45680 0.0000752 0.0039232
BRINP2 -2.587693 2.272114 19.14654 0.0020422 0.0249842
RRM2 -2.581340 4.726851 85.00166 0.0000089 0.0015377
SFRP5 -2.580538 6.389999 94.15028 0.0000059 0.0014197
GPR183 -2.580100 3.926360 50.07615 0.0000774 0.0039749
PKMYT1 -2.575518 2.462613 23.35632 0.0010938 0.0173235
ALDOC -2.573856 7.391990 80.38366 0.0000112 0.0016097
PKIA -2.570428 6.340182 81.60448 0.0000105 0.0015867
MIR1-1HG-AS1 -2.567849 3.616688 36.81472 0.0002350 0.0075473
CRABP2 -2.565913 9.841161 55.27158 0.0000533 0.0032771
SLC26A9 -2.565358 3.137698 30.38541 0.0004572 0.0108234
NEK2 -2.561090 3.131411 65.36739 0.0000254 0.0025192
TYMSOS -2.551361 2.217243 17.47788 0.0026904 0.0297094
RMI2 -2.542336 3.494177 61.93021 0.0000336 0.0028119
FERMT1 -2.540029 3.767847 40.69317 0.0001646 0.0061634
COX7C -2.538748 8.321217 29.86352 0.0004850 0.0111182
DEPDC1 -2.538447 4.163804 87.00594 0.0000081 0.0015101
CKAP2L -2.533517 3.063747 70.12482 0.0000191 0.0021905
PNMT -2.532905 2.044650 19.91435 0.0046481 0.0413085
MINCR -2.531948 2.317575 14.95233 0.0042409 0.0388960
CDK1 -2.528634 4.720155 87.35193 0.0000080 0.0015101
C11orf1 -2.523570 3.699331 26.42569 0.0007309 0.0138976
UPK1B -2.518697 3.740335 57.65215 0.0000458 0.0030761
SMIM5 -2.507403 2.351641 28.80567 0.0008846 0.0153204
GIHCG -2.502606 4.070940 29.06195 0.0005318 0.0115694
CCNB2 -2.500282 3.957803 72.93954 0.0000164 0.0019783
APOBEC2 -2.495307 6.768766 62.32141 0.0000341 0.0028119
ZNF793-AS1 -2.482754 2.441286 21.09526 0.0015121 0.0210436
ADHFE1 -2.470553 4.039047 86.42228 0.0000084 0.0015101
RPE65 -2.467311 2.822103 66.21730 0.0000409 0.0029867
PHACTR3 -2.466546 2.039413 27.35219 0.0057898 0.0473388
PRADC1 -2.464355 5.446662 35.51929 0.0002665 0.0081854
ACOT2 -2.463990 5.114293 49.12256 0.0000830 0.0041098
MTERF2 -2.454024 5.093586 67.08827 0.0000241 0.0024364
HJURP -2.451450 3.224890 26.36827 0.0007362 0.0139381
TSTD1 -2.443933 4.921833 25.47405 0.0008248 0.0147548
DUSP27 -2.443680 6.220475 13.41977 0.0057387 0.0471570
CLYBL -2.443256 2.658529 66.05325 0.0001572 0.0060712
SFRP2 -2.438680 3.032048 47.78984 0.0000919 0.0043544
LRRCC1 -2.437214 2.813535 51.67542 0.0000641 0.0036260
IDNK -2.433926 2.567916 29.80141 0.0004884 0.0111607
LINC02384 -2.433270 2.453138 22.62358 0.0012116 0.0183854
EXOC3-AS1 -2.430176 2.912271 24.60638 0.0009239 0.0157850
PHOSPHO2 -2.427786 2.270983 20.61858 0.0018242 0.0233347
KCNS2 -2.425896 2.613848 14.64476 0.0044984 0.0403073
GSG1 -2.424480 3.188673 36.02896 0.0002535 0.0079002
NUSAP1 -2.423946 4.639302 54.63118 0.0000560 0.0033764
LRRC10 -2.418899 6.726833 76.60740 0.0000135 0.0018385
TMEM141 -2.417552 5.353739 40.87874 0.0001619 0.0061221
NEBL -2.413640 8.496396 62.65125 0.0000305 0.0026939
NES -2.412128 6.009236 83.62319 0.0000095 0.0015449
TRAPPC6A -2.409063 4.164939 26.67639 0.0007084 0.0136149
SLC8A1 -2.406968 7.232354 21.61727 0.0014000 0.0200824
CENPH -2.395725 3.282142 26.98076 0.0006822 0.0132934
PHYHD1 -2.395036 3.490711 22.24569 0.0012784 0.0189503
SLC30A3 -2.395008 3.500846 73.30616 0.0000160 0.0019774
C11orf74 -2.390511 5.097256 43.62940 0.0001280 0.0052897
RCSD1 -2.389719 5.725755 40.11165 0.0001733 0.0064524
C14orf180 -2.386624 3.731630 83.44604 0.0000096 0.0015449
HSPB1 -2.385072 9.805323 28.48780 0.0005688 0.0119630
EPHX2 -2.384289 3.277717 58.93125 0.0000384 0.0029093
VIPR1 -2.382483 2.895056 26.39228 0.0007340 0.0139155
NTF4 -2.377098 2.412150 39.50176 0.0009882 0.0163644
RPA3 -2.365246 4.819416 23.48409 0.0010748 0.0171617
FN3K -2.364778 2.901139 31.40227 0.0004086 0.0101674
MRPS28 -2.358498 4.865356 35.90387 0.0002567 0.0079818
ZSCAN16-AS1 -2.356234 2.830133 18.93723 0.0021120 0.0254701
TAGLN3 -2.354777 2.218534 23.67249 0.0030785 0.0321670
UBE2C -2.349332 4.367176 29.13546 0.0005273 0.0115222
DNAAF3 -2.348180 2.676828 34.24139 0.0003030 0.0087394
HSD17B8 -2.345639 2.959449 31.66687 0.0003970 0.0100521
CRYAB -2.344243 8.985251 28.13487 0.0005931 0.0122128
TRDN-AS1 -2.340617 4.534752 58.23960 0.0000430 0.0030190
FOXM1 -2.340321 3.451918 17.45867 0.0026992 0.0297234
C17orf97 -2.335326 2.570693 50.28160 0.0004459 0.0106832
PDE6B -2.333192 3.174401 55.87002 0.0000476 0.0031122
CLIC5 -2.332800 6.040528 28.35788 0.0005776 0.0120621
TMOD1 -2.329743 7.113926 72.72280 0.0000166 0.0019783
FPGT -2.329109 2.490108 40.10933 0.0008135 0.0146726
LINC01778 -2.327603 2.512025 22.71131 0.0011967 0.0182601
LRRC52-AS1 -2.324422 3.644391 28.82426 0.0005467 0.0116920
CDCA5 -2.322462 2.828126 58.95710 0.0000791 0.0039997
TK1 -2.320187 4.733006 44.87929 0.0001156 0.0049515
MORN2 -2.319151 4.207714 23.49178 0.0010736 0.0171617
GP1BB -2.314509 2.952443 15.63393 0.0037322 0.0360061
ATP5PF -2.312218 8.040040 26.06763 0.0007646 0.0142109
COL21A1 -2.309664 4.739278 60.83793 0.0000352 0.0028119
DRD1 -2.305130 2.545329 14.66026 0.0044850 0.0402249
ACSM5 -2.303018 2.385382 53.88208 0.0015739 0.0214354
NDUFA3 -2.302154 6.004117 19.42939 0.0019524 0.0243560
BOLA1 -2.296717 3.132734 18.12030 0.0024143 0.0277539
CCND2-AS1 -2.295584 2.929593 16.76507 0.0030441 0.0319432
BIK -2.292042 4.562095 23.07729 0.0011369 0.0177094
CORO6 -2.289832 6.372772 66.69967 0.0000232 0.0023965
S100A6 -2.287949 4.171578 18.35223 0.0023233 0.0270728
HAND1 -2.281999 4.021494 50.06068 0.0000774 0.0039749
KIAA0319 -2.281731 2.523846 13.55462 0.0055830 0.0464215
COX7B -2.281664 7.853033 24.18374 0.0009774 0.0162955
CRIP2 -2.272728 9.555222 34.10054 0.0003073 0.0088094
CAMK2A -2.271184 2.230374 45.24312 0.0039582 0.0372525
TECRL -2.264283 7.866569 48.02889 0.0000902 0.0043066
ACOT1 -2.259996 2.526954 43.28432 0.0007880 0.0143980
HAND2 -2.255680 5.989330 42.70144 0.0001384 0.0055198
DERL3 -2.255450 2.906581 31.94353 0.0003853 0.0098337
BANCR -2.253846 6.871978 31.61210 0.0003994 0.0100730
NIPSNAP3B -2.253375 3.162935 39.37680 0.0001851 0.0067394
LYRM9 -2.250067 2.882413 33.06088 0.0003422 0.0093395
SRP14-AS1 -2.245190 3.680198 36.17603 0.0002499 0.0078599
BCL2A1 -2.242443 2.254108 14.98819 0.0042120 0.0387554
UNC45B -2.241744 8.454851 18.61016 0.0022271 0.0264539
CTF1 -2.240603 3.827212 30.40420 0.0004563 0.0108137
ANKRD1 -2.238789 9.282733 24.45587 0.0009425 0.0159288
KIF22 -2.232446 4.345682 70.54815 0.0000186 0.0021763
YPEL1 -2.232118 4.170625 67.48255 0.0000222 0.0023479
LYPD6 -2.228899 2.397693 15.38210 0.0039108 0.0369840
TBX20 -2.225745 3.898102 56.62588 0.0000455 0.0030701
SCHIP1 -2.222649 5.878322 71.90855 0.0000173 0.0020453
SLC2A8 -2.222631 4.835923 57.00676 0.0000451 0.0030518
PLK4 -2.221475 2.626243 16.41406 0.0032394 0.0331622
SYNJ2BP-COX16 -2.221443 3.773208 32.91179 0.0003476 0.0093542
CDC6 -2.216078 3.672923 21.20415 0.0014878 0.0208241
KCNQ2 -2.214763 3.048884 26.12628 0.0007590 0.0141490
GON7 -2.209077 3.519188 23.17055 0.0011223 0.0175621
ACAT1 -2.204879 6.880535 69.95317 0.0000193 0.0021988
VSNL1 -2.201836 4.885539 56.22627 0.0000475 0.0031122
CDC20 -2.200800 3.810945 61.78922 0.0000312 0.0027335
ACADSB -2.198825 4.134325 16.78102 0.0030355 0.0318708
SELENOW -2.198793 9.304079 29.34283 0.0005148 0.0113764
LINC00526 -2.197931 2.732049 16.93661 0.0029539 0.0312987
COX6C -2.195835 8.360781 23.13352 0.0011281 0.0176244
REXO5 -2.195596 3.426408 20.84830 0.0015689 0.0214354
SSPN -2.183134 4.659579 27.07836 0.0006740 0.0131871
DAND5 -2.181966 2.602316 24.45002 0.0009432 0.0159288
RBMS3-AS3 -2.180075 2.357659 22.80648 0.0026288 0.0293933
HMGCLL1 -2.178475 3.329774 63.32700 0.0000284 0.0026266
LINC00880 -2.177140 4.941708 58.97843 0.0000377 0.0029093
C10orf71 -2.176344 2.517078 13.39051 0.0057732 0.0472623
HMGN2 -2.174406 7.534315 37.74387 0.0002152 0.0072678
MYL9 -2.170793 9.804863 43.82020 0.0001213 0.0051481
ROGDI -2.167941 5.631528 44.24487 0.0001217 0.0051481
PLN -2.167092 10.586009 32.98622 0.0003449 0.0093542
HAND2-AS1 -2.167011 5.831762 64.36575 0.0000266 0.0025505
PCBD1 -2.167003 5.394227 27.40924 0.0006473 0.0128954
MPC1 -2.165892 6.005173 24.23629 0.0009706 0.0162227
TAFA2 -2.164442 2.255294 24.39671 0.0050199 0.0433758
DNAJC28 -2.164137 2.445701 24.11364 0.0017714 0.0228985
INKA2 -2.162963 4.047909 45.79497 0.0001074 0.0047481
USH1C -2.162887 2.287685 20.73651 0.0042933 0.0391865
NDUFS6 -2.162245 6.404731 29.01831 0.0005345 0.0115897
ADCY5 -2.158902 6.403468 18.51693 0.0022613 0.0265902
MDP1 -2.154549 4.111410 26.29860 0.0007426 0.0139891
PMEL -2.153426 3.412220 49.85708 0.0000736 0.0038614
MTURN -2.152774 4.617683 56.33443 0.0000460 0.0030777
LINC01351 -2.148929 2.241988 28.24087 0.0052656 0.0448276
LINC02762 -2.143704 4.734591 28.17354 0.0005904 0.0121937
ULK4 -2.138354 3.556534 52.49176 0.0000597 0.0034670
DLGAP1-AS1 -2.134387 2.569413 15.58070 0.0037691 0.0361948
DES -2.134094 7.311249 53.44978 0.0000559 0.0033764
TMEM97 -2.134051 4.002616 64.21022 0.0000269 0.0025570
SLC5A1 -2.133719 4.807662 18.20450 0.0023808 0.0275223
PRC1 -2.133292 4.849762 29.60058 0.0004998 0.0112467
DECR1 -2.132021 6.754908 53.62447 0.0000559 0.0033764
GLIDR -2.130896 3.395435 38.39637 0.0002025 0.0070229
HMGN5 -2.130325 2.776836 22.89057 0.0011669 0.0178976
SHCBP1 -2.129381 3.220118 17.35530 0.0027474 0.0300854
ATP5ME -2.123243 6.673001 20.47854 0.0016591 0.0220280
SYNM -2.122636 5.032839 14.79312 0.0043718 0.0395976
UQCRQ -2.122164 8.188141 23.99711 0.0010023 0.0164998
NDUFB2 -2.118844 7.042373 23.87766 0.0010186 0.0166153
CMC4 -2.118674 4.267070 25.08004 0.0008681 0.0151960
ITM2A -2.118308 3.567860 27.99204 0.0006033 0.0123602
BEX2 -2.111248 4.212815 32.95306 0.0003461 0.0093542
MGST3 -2.109753 8.346264 21.65019 0.0013933 0.0200007
ANAPC16 -2.104280 7.102962 35.44008 0.0002686 0.0082305
MRPL53 -2.101326 5.157360 19.83226 0.0018327 0.0233988
NAP1L3 -2.099201 5.370958 37.98851 0.0002103 0.0071578
IL20RA -2.099056 2.714177 36.71103 0.0005470 0.0116920
ATP5MC3 -2.098677 8.587440 29.02713 0.0005340 0.0115897
GUCY1A1 -2.098464 8.470145 45.22582 0.0001080 0.0047643
MYBPC3 -2.098119 8.888559 15.80577 0.0036160 0.0353217
CDKN2C -2.096007 2.806192 27.16126 0.0006672 0.0130934
KLHL3 -2.095120 5.065742 21.68043 0.0013872 0.0199564
EFCAB7 -2.091420 3.359217 50.90181 0.0000656 0.0036581
GTSE1 -2.089318 2.842977 45.09877 0.0002398 0.0076380
ASB2 -2.088868 6.945506 37.00136 0.0002308 0.0075122
EMP2 -2.088006 6.850257 31.32778 0.0004119 0.0101815
GNG7 -2.087833 3.678315 64.54015 0.0000264 0.0025481
DOK7 -2.086878 4.289914 73.31434 0.0000160 0.0019774
PHACTR1 -2.086106 4.967612 49.77250 0.0000759 0.0039278
PLPP7 -2.082147 5.797028 56.29100 0.0000446 0.0030414
FAM229B -2.080910 5.638910 32.65186 0.0003573 0.0094353
CDCA7 -2.075812 2.507710 19.71112 0.0020206 0.0248592
HIGD2A -2.075338 6.919949 18.70036 0.0021946 0.0261471
ICA1 -2.073635 4.836517 68.83267 0.0000205 0.0022828
ATP5PD -2.070352 7.400018 25.90665 0.0007804 0.0143064
PARP1 -2.069997 7.027387 33.84833 0.0003154 0.0088535
TMEM144 -2.068687 3.363263 57.90221 0.0000401 0.0029548
SH3RF2 -2.067586 4.951165 51.65734 0.0000642 0.0036260
DGCR6 -2.064497 4.510378 28.97295 0.0005373 0.0116181
NDUFC1 -2.062849 6.706193 19.79048 0.0018447 0.0234906
ACYP1 -2.061079 3.705755 16.05494 0.0034555 0.0345052
COX8A -2.061003 7.174523 18.02479 0.0024531 0.0280842
MYLK -2.060309 9.251826 39.45907 0.0001812 0.0066224
FAM20A -2.059499 2.536403 23.34206 0.0016766 0.0222278
PLCXD3 -2.058581 4.883096 45.79334 0.0001064 0.0047457
ABHD11 -2.056984 3.790402 36.09377 0.0002519 0.0078889
MMP15 -2.056655 6.566182 23.07605 0.0011371 0.0177094
ST7-AS1 -2.056492 2.512928 37.15366 0.0019371 0.0241803
NSMCE4A -2.054613 5.063454 55.80641 0.0000461 0.0030777
INKA2-AS1 -2.054012 2.680850 43.39229 0.0007955 0.0144810
NEXN -2.052929 7.854613 26.66831 0.0007091 0.0136149
ATP5MF -2.049363 6.800521 20.18405 0.0017356 0.0225697
PPP1R14C -2.047443 7.214625 47.84907 0.0000868 0.0042247
NIFK-AS1 -2.046841 2.901511 41.10360 0.0002045 0.0070518
ERH -2.046144 6.396813 26.20089 0.0007518 0.0140776
HACD1 -2.043966 7.480174 26.17384 0.0007544 0.0140989
PET100 -2.043188 5.273546 19.17708 0.0020323 0.0249403
SMDT1 -2.037491 5.542199 24.53255 0.0009330 0.0158372
RDH5 -2.037272 3.028846 23.52853 0.0010683 0.0171617
DNAJC15 -2.036522 4.760353 33.85317 0.0003152 0.0088535
PIFO -2.030697 3.565426 34.43401 0.0002971 0.0086644
ETFRF1 -2.029499 4.676854 20.12125 0.0017525 0.0226838
SKA3 -2.028284 2.472653 24.59829 0.0028315 0.0305793
GJA5 -2.025339 5.790669 22.33501 0.0012622 0.0188791
DHRS11 -2.024969 2.355453 31.98705 0.0046921 0.0415305
GSTM4 -2.024015 5.693714 36.46172 0.0002431 0.0077321
ATP5MC1 -2.023177 6.647563 21.24909 0.0014779 0.0207022
MYL3 -2.022303 8.201414 31.77318 0.0003925 0.0099627
TIMM8B -2.021806 5.967973 25.75849 0.0007953 0.0144810
ATP5MPL -2.020557 7.320474 20.41067 0.0016764 0.0222278
CHCHD5 -2.019536 3.888336 17.55777 0.0026540 0.0295236
IL17B -2.019427 2.383419 20.90870 0.0041069 0.0381662
PPP1R3C -2.018053 4.783392 29.60422 0.0004996 0.0112467
SVIP -2.011910 3.910878 16.67467 0.0030929 0.0322491
HADH -2.010848 5.595895 68.67077 0.0000207 0.0022838
UQCR10 -2.010785 7.642238 20.76159 0.0015895 0.0215560
CHURC1-FNTB -2.009534 3.707609 30.17326 0.0004683 0.0109265
FANCL -2.006840 4.456246 56.40377 0.0000443 0.0030414
CPVL -2.005104 6.774119 60.13375 0.0000346 0.0028119
PLK1 -2.000453 3.879544 55.08925 0.0000484 0.0031436
ACOT13 -2.000114 5.847783 30.46547 0.0004532 0.0107527
PTBP3 2.004432 5.518912 29.26607 0.0005194 0.0114385
TGFBI 2.008175 8.222606 22.90922 0.0011639 0.0178976
RLF 2.009219 6.916310 24.51223 0.0009355 0.0158515
ERO1A 2.009337 6.150180 39.92083 0.0001763 0.0065139
MYD88 2.019954 5.073590 30.86736 0.0004333 0.0104852
LRIG3 2.022030 4.074215 23.79939 0.0010295 0.0167509
GTF2IRD1 2.022119 5.320018 40.71978 0.0001642 0.0061607
PIM3 2.022238 5.524202 64.94521 0.0000257 0.0025377
RSRC2 2.024864 7.386379 58.53508 0.0000384 0.0029093
PIGA 2.025300 4.525591 33.41666 0.0003297 0.0091468
ARRDC2 2.028687 2.975729 46.06784 0.0001172 0.0050104
CASP4 2.031420 4.582159 45.33682 0.0001110 0.0048176
KCNE4 2.032976 5.291654 43.40793 0.0001304 0.0053098
TLE1 2.036129 5.850678 32.45804 0.0003647 0.0095666
EGR1 2.037634 7.201431 39.15933 0.0001888 0.0068231
HRH1 2.039099 4.520897 66.50932 0.0000235 0.0024106
EVC2 2.040074 3.251847 28.55813 0.0005641 0.0118834
H2BC5 2.042077 3.796569 33.39466 0.0003305 0.0091468
LIPG 2.043150 3.120983 30.06482 0.0004741 0.0110002
EMP1 2.044095 3.812334 38.37499 0.0002029 0.0070229
HAPLN3 2.047483 4.194068 74.36986 0.0000152 0.0019319
PIK3CD 2.048266 3.513463 26.05156 0.0007662 0.0142109
DBP 2.048628 4.124211 59.13743 0.0000369 0.0028841
ADM2 2.052314 3.681901 35.21260 0.0002748 0.0083105
BAIAP2L1 2.054319 3.244316 25.61844 0.0008097 0.0146300
PFKFB3 2.054620 6.220168 15.56250 0.0037818 0.0362354
TRIM22 2.055730 6.297457 25.72451 0.0007987 0.0145127
PDZD2 2.058617 3.287078 41.29298 0.0001562 0.0060442
ZNF844 2.061578 3.110554 21.42606 0.0014398 0.0205036
ITGA2 2.062052 5.779381 36.02532 0.0002536 0.0079002
DOK5 2.067119 4.379998 72.74209 0.0000165 0.0019783
SKIL 2.067251 6.890339 71.06788 0.0000181 0.0021288
PCSK9 2.069441 2.878845 35.17666 0.0002758 0.0083139
RAPGEF2 2.072268 6.336223 37.49660 0.0002202 0.0073354
NPIPB15 2.073422 2.578592 24.83420 0.0011091 0.0174534
CLCF1 2.075358 2.714797 34.93737 0.0004695 0.0109413
RGS16 2.075771 2.246447 14.59476 0.0056342 0.0465904
ADCY7 2.076348 3.765286 32.91226 0.0003476 0.0093542
KLF9 2.079559 2.831800 31.39751 0.0004088 0.0101674
SQSTM1 2.082316 10.098863 57.79548 0.0000403 0.0029646
FGF7 2.083364 5.050689 46.79790 0.0000988 0.0045511
SH3RF1 2.084813 6.094909 27.20199 0.0006639 0.0130802
CDH6 2.086026 3.842225 55.08953 0.0000487 0.0031438
HOXA-AS2 2.088457 3.095199 35.63492 0.0002635 0.0081436
NBPF14 2.093447 5.379842 64.62730 0.0000262 0.0025480
UBASH3B 2.093595 3.201016 39.89774 0.0001766 0.0065151
ZNF317 2.095386 6.258907 18.24073 0.0023665 0.0274296
IFRD1 2.095692 6.835812 61.33781 0.0000321 0.0027505
PDE7A 2.096324 5.599562 37.26773 0.0002251 0.0074103
TMEM87B 2.099924 5.543321 38.74301 0.0001961 0.0069235
DPP4 2.104114 3.978669 21.26956 0.0014735 0.0207016
C1QTNF1 2.109298 4.248291 43.41985 0.0001303 0.0053098
MVP 2.111094 6.994655 42.08814 0.0001458 0.0056996
ERRFI1 2.113944 7.003143 24.13875 0.0009833 0.0163127
KLF11 2.114600 5.413462 17.94407 0.0024864 0.0283832
NRG3 2.120995 3.509814 54.36167 0.0000514 0.0032300
SLC38A5 2.122949 2.645344 36.38028 0.0005832 0.0120940
ARHGAP20 2.123484 2.634645 24.11675 0.0009863 0.0163457
THSD1 2.128001 2.363420 20.24808 0.0027872 0.0302996
IL33 2.129479 5.178257 68.35190 0.0000211 0.0022998
TENT5C 2.132303 3.190938 24.57125 0.0009282 0.0158242
RXFP1 2.133374 2.598005 17.13141 0.0028556 0.0307207
NBPF26 2.135125 5.269142 26.29526 0.0007430 0.0139891
THY1 2.139841 7.881571 48.91955 0.0000806 0.0040457
TYMP 2.142315 3.825328 27.48119 0.0006417 0.0128615
GBP3 2.142594 4.570524 26.94510 0.0006852 0.0133387
STARD13 2.146103 5.337618 26.34210 0.0007386 0.0139479
LDB2 2.155333 4.882540 55.32438 0.0000501 0.0031761
EIF2AK2 2.155542 6.387405 27.20722 0.0006635 0.0130802
HS6ST2 2.158807 2.247820 20.55080 0.0043804 0.0395997
ZBTB10 2.166943 5.196433 23.02788 0.0011448 0.0177862
CHD1 2.167425 6.450497 49.55368 0.0000799 0.0040307
GADD45B 2.169566 7.554465 59.97477 0.0000350 0.0028119
NFKBID 2.170539 2.547989 52.98504 0.0008309 0.0148364
SEC24A 2.171192 6.533926 13.53523 0.0056050 0.0465458
HFE 2.173138 2.553298 44.69194 0.0008030 0.0145489
KCNAB1 2.174609 3.216456 68.84353 0.0000205 0.0022828
SEL1L3 2.178554 6.491276 17.09245 0.0028749 0.0308611
LRRC8E 2.181391 2.746993 21.81094 0.0013611 0.0197421
PTGIS 2.183773 8.541022 45.82255 0.0001059 0.0047334
ACHE 2.184265 4.274795 76.04896 0.0000139 0.0018792
NEDD9 2.198391 7.346351 22.41278 0.0012483 0.0187707
TBC1D2 2.199856 2.787065 31.87433 0.0003882 0.0098882
IL1RL1 2.200511 7.940512 39.48969 0.0001832 0.0066833
ATP8B1 2.201638 4.908575 24.29311 0.0009632 0.0161408
SMURF1 2.206765 6.367100 14.95457 0.0042391 0.0388960
CACTIN 2.216597 5.371437 35.65443 0.0002630 0.0081408
WAKMAR2 2.221539 2.255501 35.50517 0.0033638 0.0340250
GPBP1 2.221672 7.846399 45.51049 0.0001098 0.0048017
SNAPC1 2.224079 6.031346 74.62952 0.0000150 0.0019306
CLK4 2.230614 5.934948 46.22436 0.0001038 0.0046814
MFAP3L 2.230693 3.271002 25.00516 0.0008766 0.0152898
SPRED3 2.232555 2.258711 31.46815 0.0032174 0.0330170
FOXN2 2.235189 4.821019 38.30894 0.0002041 0.0070518
SMOX 2.238389 4.386918 63.07335 0.0000291 0.0026381
DTX3L 2.238600 4.502182 39.29451 0.0001865 0.0067647
TNFAIP2 2.246920 2.435379 31.99143 0.0011633 0.0178976
DUSP6 2.247526 6.615571 59.10035 0.0000387 0.0029093
ETV4 2.255293 3.389742 51.16339 0.0000698 0.0037609
DRAM1 2.255817 5.547865 49.94757 0.0000781 0.0039752
RASGRF2 2.257768 3.281691 27.15870 0.0006674 0.0130934
ARSI 2.258777 3.445717 57.34857 0.0000428 0.0030190
SLC7A5 2.268056 8.820527 25.50067 0.0008220 0.0147311
SPRED1 2.268266 5.631474 32.44575 0.0003652 0.0095666
STEAP1 2.269506 2.158776 34.45582 0.0046983 0.0415667
HES1 2.272304 6.315384 48.47497 0.0000872 0.0042349
RBM15 2.273480 4.733079 22.39799 0.0012509 0.0187947
ITGA4 2.280581 7.210732 23.24107 0.0011114 0.0174687
DDIT3 2.282792 6.698829 47.72524 0.0000923 0.0043655
GPR176 2.287500 6.829438 25.25024 0.0008491 0.0150044
BRPF1 2.289519 5.016377 18.25805 0.0023597 0.0273672
SERPINB8 2.291079 4.970055 82.51326 0.0000101 0.0015540
DUSP1 2.292234 8.485314 75.91168 0.0000140 0.0018797
TRIM25 2.294127 4.596770 23.47330 0.0010764 0.0171659
CFB 2.294208 3.185792 21.59213 0.0014052 0.0201416
ALDH1A3 2.304578 5.569875 17.07360 0.0028843 0.0309039
HTR7 2.306582 3.975230 29.33506 0.0005153 0.0113764
SULF1 2.309025 10.514876 14.30185 0.0048089 0.0422406
SLC2A9 2.313958 2.664464 51.53580 0.0002084 0.0071561
TAP1 2.318335 6.931737 27.26981 0.0006584 0.0130241
PDK4 2.321624 4.492490 56.64808 0.0000484 0.0031436
EPHA2 2.323694 7.567711 27.87603 0.0006118 0.0124792
SLC43A3 2.324096 3.546745 51.56179 0.0000694 0.0037609
SLC22A3 2.328724 4.729065 37.98477 0.0002104 0.0071578
IRAK2 2.332145 2.903430 52.71759 0.0000589 0.0034522
TRIM38 2.333957 4.789839 61.01720 0.0000353 0.0028119
INTS6 2.335218 6.513688 36.35409 0.0002457 0.0077752
CD44 2.340378 7.554509 45.66604 0.0001085 0.0047730
ELF3 2.340595 4.964933 84.78612 0.0000090 0.0015377
BCL3 2.352478 5.600504 65.95346 0.0000252 0.0025180
BCAR3 2.356021 5.790211 38.71697 0.0001966 0.0069261
ULBP2 2.358103 3.957069 80.46097 0.0000111 0.0016097
JUN 2.358727 8.861739 32.15737 0.0003766 0.0097804
MCTP2 2.360615 3.508561 32.70630 0.0003552 0.0094353
LSMEM1 2.361432 2.317843 45.62247 0.0015010 0.0209329
AMIGO2 2.368723 8.003288 43.69275 0.0001274 0.0052731
ADAM32 2.376574 2.341232 46.01163 0.0012660 0.0189031
APOL1 2.379876 4.122219 21.56230 0.0014113 0.0201856
IRF1 2.379943 4.992209 87.12418 0.0000081 0.0015101
INHBA 2.383219 8.306131 78.67403 0.0000121 0.0017024
MALL 2.383326 2.659139 41.05437 0.0001594 0.0060992
FRMD6 2.387872 6.891291 14.68130 0.0044669 0.0401342
RGS4 2.388592 7.191836 57.83783 0.0000446 0.0030414
CIART 2.392362 4.790032 92.17636 0.0000065 0.0014424
CREBRF 2.394751 6.655744 61.63792 0.0000343 0.0028119
HLA-E 2.405630 7.998819 48.34451 0.0000881 0.0042472
TPBG 2.407003 6.893303 69.75091 0.0000198 0.0022405
TG 2.407486 3.313804 64.08243 0.0000274 0.0025570
TNFRSF1B 2.408509 2.494308 40.14760 0.0004310 0.0104419
CXCL6 2.410656 2.592254 46.90449 0.0002179 0.0073154
TET3 2.410728 4.493949 52.52010 0.0000648 0.0036353
NR6A1 2.414602 2.865905 52.70812 0.0000604 0.0034872
MYO3A 2.414730 2.342404 33.47029 0.0011067 0.0174366
PARP9 2.414755 5.806204 16.66523 0.0030981 0.0322639
BCL6 2.422277 6.040827 70.56460 0.0000190 0.0021905
INSYN2B 2.430209 2.488640 42.73621 0.0004134 0.0101815
NBPF19 2.433163 3.774509 53.83972 0.0000591 0.0034529
LOXL2 2.435605 9.183272 31.59394 0.0004002 0.0100799
HIVEP1 2.437602 6.216610 37.05956 0.0002296 0.0075043
MAPK13 2.450262 2.028206 22.03778 0.0055114 0.0462644
NEFM 2.456494 2.322909 25.11623 0.0010629 0.0171617
SOX17 2.458071 2.337055 58.62437 0.0009577 0.0161040
DUSP4 2.462814 3.126499 58.04295 0.0000427 0.0030190
SLCO2A1 2.466396 2.839009 37.82173 0.0002136 0.0072524
CA12 2.469995 4.680373 66.11578 0.0000262 0.0025480
PDE10A 2.477695 5.789936 54.34658 0.0000571 0.0033950
KLF4 2.478537 2.201813 47.66737 0.0019818 0.0245703
PTGER4 2.483473 2.339761 35.38493 0.0008789 0.0152928
IL15RA 2.483720 2.576531 27.93078 0.0006078 0.0124300
KLF5 2.485018 5.690175 73.25404 0.0000166 0.0019783
BHLHE40 2.496503 7.578998 58.09862 0.0000445 0.0030414
EDEM1 2.498534 5.605145 25.98581 0.0007726 0.0142520
MEDAG 2.503234 3.778340 64.17896 0.0000292 0.0026381
TIGD3 2.508575 2.188260 32.33343 0.0019804 0.0245703
SLC2A3 2.509515 7.984835 31.98997 0.0003834 0.0098214
FNIP2 2.511309 7.557486 28.91908 0.0005407 0.0116472
LOXL3 2.511423 3.727307 62.42745 0.0000329 0.0027841
TRAF1 2.514945 3.056460 53.39919 0.0000610 0.0035080
KLF10 2.515128 7.427442 50.13561 0.0000770 0.0039749
UGCG 2.518274 7.585201 83.56366 0.0000096 0.0015449
VEGFC 2.535167 4.635154 94.71748 0.0000058 0.0014052
CPM 2.545456 3.022765 67.41990 0.0000223 0.0023479
PHLDA2 2.549979 5.303923 43.22775 0.0001324 0.0053487
OVGP1 2.567849 2.209877 35.06004 0.0014456 0.0205290
SPINT1 2.569089 2.654571 59.90095 0.0000670 0.0037034
APOL6 2.571367 3.725652 28.88805 0.0005427 0.0116535
STC2 2.574370 8.153217 47.92961 0.0000909 0.0043208
CSF1 2.579403 6.467006 103.92047 0.0000040 0.0012869
ADIRF-AS1 2.579661 2.075189 18.68391 0.0030687 0.0321160
F2RL1 2.589487 4.255967 53.54420 0.0000603 0.0034872
CD101 2.589927 2.004320 17.59860 0.0043811 0.0395997
HERC6 2.604753 5.322727 13.54169 0.0055977 0.0465044
IL1R1 2.605356 7.513133 24.61197 0.0009232 0.0157850
TNFSF9 2.605547 3.160242 47.56645 0.0000935 0.0044085
GRB7 2.610120 2.239059 26.62211 0.0010549 0.0170510
BMPR1B 2.619521 2.968540 62.37361 0.0000318 0.0027505
TNFRSF10D 2.620613 7.480225 14.94479 0.0042470 0.0389248
HOXA5 2.628181 3.550076 65.55187 0.0000275 0.0025578
PMAIP1 2.637589 5.368933 70.49822 0.0000210 0.0022998
TMED7-TICAM2 2.639298 4.595094 49.37553 0.0000815 0.0040633
PARP14 2.642709 6.036682 14.89076 0.0042909 0.0391865
H2BC8 2.643823 2.446299 49.98735 0.0002391 0.0076380
SGK1 2.647606 8.446304 81.45867 0.0000106 0.0015867
SBNO2 2.656249 4.523733 36.87898 0.0002336 0.0075257
PDCD1LG2 2.657190 3.062061 37.68423 0.0002164 0.0072960
ITGA5 2.665103 9.258279 24.97348 0.0008803 0.0152928
KCNN1 2.667134 2.217189 49.10990 0.0010080 0.0165225
SELPLG 2.668810 3.424445 50.72737 0.0000737 0.0038614
SP100 2.676217 6.869313 49.92929 0.0000782 0.0039752
SERPINB2 2.677729 2.534626 32.68863 0.0003559 0.0094353
GABRR2 2.682761 2.202704 29.53987 0.0010748 0.0171617
WNK4 2.682955 3.808848 82.80079 0.0000099 0.0015449
TM4SF1 2.691544 5.916868 102.61484 0.0000042 0.0012883
BMP6 2.691649 5.361842 39.69598 0.0001799 0.0065847
CCL2 2.692769 7.847590 52.45024 0.0000652 0.0036429
CHD2 2.697284 7.759830 61.58868 0.0000357 0.0028350
ADGRE5 2.699674 4.148737 62.43113 0.0000339 0.0028119
INHBE 2.700693 3.138498 27.32567 0.0006539 0.0129541
ZBTB21 2.703003 4.756237 52.63773 0.0000643 0.0036260
CPA4 2.708803 8.661667 57.24498 0.0000470 0.0031122
H2BC18 2.711889 1.912383 47.22384 0.0053097 0.0450662
SLC19A2 2.718296 4.679205 69.11184 0.0000230 0.0023965
PLOD2 2.720926 9.054149 33.04360 0.0003428 0.0093435
PRR5L 2.722209 2.279041 41.67201 0.0005820 0.0120858
BHLHE41 2.722265 5.510344 79.09856 0.0000128 0.0017608
PTGES 2.722689 4.499698 47.92230 0.0000909 0.0043208
IP6K3 2.727148 3.257753 58.45228 0.0000435 0.0030255
JUNB 2.744661 8.839775 69.48414 0.0000218 0.0023298
RBM47 2.744715 2.345884 34.59026 0.0003440 0.0093542
CCNL1 2.752683 7.774751 110.61420 0.0000031 0.0012769
ARHGEF28 2.759261 2.802980 47.49817 0.0000940 0.0044212
GALNT12 2.762916 4.193289 63.99295 0.0000309 0.0027158
RFLNA 2.764764 4.147928 84.39458 0.0000095 0.0015449
SPHK1 2.772888 6.222188 123.11496 0.0000020 0.0010944
PER1 2.773211 6.060084 87.44212 0.0000083 0.0015101
FOSL1 2.786567 3.793474 112.58099 0.0000029 0.0012769
TMEM200A 2.789991 6.447756 89.28898 0.0000075 0.0015101
KCNG1 2.794918 5.266295 87.31263 0.0000083 0.0015101
APOL3 2.797154 2.342614 21.18435 0.0014922 0.0208704
ARRDC3 2.797668 6.423077 42.94122 0.0001356 0.0054314
CDC14A 2.798065 4.378705 46.86708 0.0000987 0.0045511
SLC5A3 2.807390 6.175750 45.49239 0.0001100 0.0048017
GPR87 2.819893 2.113681 45.56112 0.0012731 0.0189112
HAP1 2.828557 1.875954 17.09753 0.0050469 0.0435322
ATF3 2.834749 6.181991 106.16959 0.0000037 0.0012869
LOX 2.837510 10.821083 42.10166 0.0001456 0.0056996
ICAM1 2.844774 5.364546 70.47057 0.0000214 0.0023028
ANXA10 2.847749 1.829139 51.94006 0.0062174 0.0495546
H2BC6 2.848198 1.878000 30.25758 0.0047705 0.0419783
SAMD9L 2.854908 3.920715 16.87209 0.0029874 0.0315855
ATP10A 2.857127 4.766572 49.82133 0.0000788 0.0039967
PTGS1 2.871569 4.109720 40.56185 0.0001665 0.0062233
PPP1R15A 2.888216 8.511152 94.88975 0.0000058 0.0014052
FAM83G 2.890823 4.646828 39.07453 0.0001903 0.0068633
IFIT1 2.897333 7.041470 17.89687 0.0025062 0.0285093
TMEM158 2.907377 4.242491 89.36416 0.0000077 0.0015101
IPMK 2.909372 3.921477 59.40324 0.0000409 0.0029867
TMEM119 2.916719 2.770240 42.17314 0.0001448 0.0056924
FOS 2.924209 8.202713 111.89453 0.0000030 0.0012769
GCH1 2.930393 3.821751 40.90273 0.0001616 0.0061210
ADCY10 2.934266 2.007223 19.27309 0.0020014 0.0246730
AGTR1 2.936738 1.985556 31.28869 0.0020865 0.0253049
ZSWIM4 2.947280 3.828771 35.24651 0.0002738 0.0083105
SLC20A1 2.959516 8.545497 43.95958 0.0001246 0.0052069
OSMR 2.968027 6.966265 28.35249 0.0005780 0.0120621
LINC01119 2.971468 2.172242 58.56300 0.0005557 0.0118139
TNFRSF6B 2.973553 2.364744 31.54205 0.0004024 0.0100851
TLR4 2.977475 4.828423 42.32298 0.0001429 0.0056540
NPIPB6 2.977480 3.411860 58.29854 0.0000439 0.0030414
IL6 2.982850 4.006756 88.50850 0.0000082 0.0015101
TMEM255B 2.982863 3.190498 86.45227 0.0000084 0.0015101
APLN 2.991301 1.846589 47.13043 0.0042620 0.0390111
ADM5 2.995367 1.815252 39.98235 0.0050671 0.0436486
PFKFB4 2.996145 4.417500 61.31929 0.0000363 0.0028708
EGR2 2.997124 4.464698 91.86878 0.0000071 0.0015101
FNDC11 3.003023 2.063081 24.45838 0.0010925 0.0173168
RELB 3.007213 5.745798 101.00085 0.0000046 0.0012883
TAF4B 3.014949 3.286624 92.77776 0.0000063 0.0014380
SH2B3 3.016999 5.564816 47.23800 0.0000959 0.0044695
PCDH8 3.023577 2.109310 32.17253 0.0007661 0.0142109
TFPI2 3.045211 7.289627 76.41806 0.0000156 0.0019665
SAMHD1 3.052257 6.155858 33.54926 0.0003252 0.0090658
GFPT2 3.053507 7.114968 55.27068 0.0000536 0.0032875
IL12A 3.074159 1.954999 35.21462 0.0018710 0.0237584
NFKB2 3.074821 5.527933 111.23830 0.0000030 0.0012769
MYO10 3.075920 5.670992 51.52942 0.0000696 0.0037609
SLC25A25 3.094355 5.643307 49.35799 0.0000816 0.0040633
PAPPA 3.106189 7.907271 78.09810 0.0000144 0.0019055
KCNJ6 3.107220 3.589969 66.83040 0.0000262 0.0025480
PLA2G4A 3.110495 4.074551 82.71147 0.0000115 0.0016253
IDI2-AS1 3.112656 1.917110 26.86395 0.0021878 0.0261013
CDC42EP2 3.119416 4.920009 43.94273 0.0001248 0.0052069
NBPF10 3.123370 5.585064 58.08067 0.0000445 0.0030414
PARP10 3.156709 4.824737 34.79916 0.0002864 0.0084898
NFKBIZ 3.159083 7.121925 67.68861 0.0000249 0.0025076
CD83 3.173820 4.440632 100.41670 0.0000049 0.0013075
PER2 3.177066 3.949798 105.20435 0.0000038 0.0012869
SUSD3 3.177775 1.913574 49.11554 0.0019182 0.0240671
NPIPB9 3.187425 3.056459 85.96106 0.0000090 0.0015377
TNFSF4 3.194547 4.449263 39.82799 0.0001777 0.0065217
CSRNP1 3.209089 6.393243 77.56168 0.0000148 0.0019306
LIF 3.218333 3.313136 68.51894 0.0000238 0.0024308
CDCP1 3.221546 3.220219 40.95561 0.0001608 0.0061107
CFAP43 3.236729 2.165087 49.14447 0.0002905 0.0085601
IFI6 3.245873 9.114637 16.84248 0.0030030 0.0316902
CYP1B1 3.250809 7.104491 78.42151 0.0000141 0.0018880
HELZ2 3.260663 3.448995 29.49406 0.0005059 0.0113044
IFIH1 3.261873 4.786974 19.15159 0.0020406 0.0249842
MAP3K8 3.271886 4.537469 125.90809 0.0000018 0.0010564
DDX58 3.283058 6.746199 25.90700 0.0007804 0.0143064
MYCT1 3.289963 2.046555 40.95518 0.0006164 0.0125473
CDH16 3.290525 1.742021 60.36658 0.0044961 0.0403046
SIX4 3.320190 3.895493 92.89530 0.0000071 0.0015101
NR1D1 3.343418 4.357002 106.64788 0.0000039 0.0012869
IFITM1 3.349915 8.961878 31.36005 0.0004105 0.0101815
MAFF 3.370586 5.316654 148.11264 0.0000009 0.0008348
TRIM14 3.388914 4.091813 23.23787 0.0011119 0.0174687
PTPRN 3.400174 5.267114 87.46905 0.0000092 0.0015377
PLAUR 3.405416 6.861024 104.07963 0.0000047 0.0012892
ANKS4B 3.408031 2.135298 51.93580 0.0002362 0.0075737
NFKBIA 3.417202 8.391397 107.47928 0.0000038 0.0012869
BST2 3.420476 7.307547 28.62527 0.0005597 0.0118432
CDK5R1 3.428745 4.033448 61.98541 0.0000348 0.0028119
MLKL 3.442330 2.640487 32.79267 0.0003520 0.0094101
GIPC3 3.444105 2.761143 35.57037 0.0002652 0.0081698
NPC1L1 3.472580 1.880101 42.48278 0.0013512 0.0196696
MYRFL 3.473980 3.090140 112.05350 0.0000029 0.0012769
CXCR1 3.476321 1.651404 65.32856 0.0057019 0.0469329
PCDH15 3.477425 2.628085 60.98567 0.0000370 0.0028841
SNAI1 3.501171 3.290060 116.77807 0.0000025 0.0012520
ANKRD33B 3.521136 3.588617 84.47745 0.0000106 0.0015867
USP18 3.526600 5.093084 22.54242 0.0012256 0.0185422
PTX3 3.554543 8.390962 123.98638 0.0000020 0.0010944
NFATC2 3.555795 3.933467 108.29201 0.0000037 0.0012869
SERPINE1 3.556188 10.606702 103.55315 0.0000043 0.0012883
SLC2A5 3.566019 3.689098 139.12562 0.0000012 0.0008663
MICB 3.587570 4.564095 128.86532 0.0000017 0.0010207
ZBTB2 3.600436 6.397979 128.33353 0.0000018 0.0010564
LINC01823 3.619946 1.710207 70.23833 0.0032122 0.0329840
SLC12A8 3.620080 6.029256 138.55951 0.0000012 0.0008663
SAMD9 3.629801 5.398846 25.32834 0.0008405 0.0149144
IRF8 3.652257 3.459020 129.81346 0.0000016 0.0010207
STC1 3.653529 4.152861 114.32324 0.0000030 0.0012769
APCDD1L 3.695406 2.896546 63.34529 0.0000321 0.0027505
IFI27 3.706511 5.887802 13.31120 0.0058680 0.0476806
GAL3ST1 3.711185 2.265829 88.74739 0.0000349 0.0028119
SRGN 3.730504 3.888739 90.97631 0.0000079 0.0015101
BIRC3 3.746385 3.629215 142.35202 0.0000011 0.0008348
NR4A3 3.746540 4.579866 99.92274 0.0000055 0.0014052
SAA1 3.753236 2.059358 53.31650 0.0001962 0.0069235
NXPE2 3.755393 2.052772 74.76876 0.0002086 0.0071561
CXCL8 3.764355 3.864053 93.14546 0.0000072 0.0015101
ACTBL2 3.808624 3.464013 75.19980 0.0000166 0.0019783
FOSB 3.811074 3.547716 90.06315 0.0000082 0.0015101
TNC 3.811429 8.709608 29.60629 0.0004994 0.0112467
SPOCD1 3.815799 3.920872 142.58956 0.0000011 0.0008348
CXCL3 3.824323 3.424551 90.05022 0.0000083 0.0015101
HAS1 3.840127 2.411141 95.33842 0.0000057 0.0014052
NR4A1AS 3.850720 2.651442 58.71612 0.0000427 0.0030190
ZC3H12A 3.904393 5.451827 178.02256 0.0000004 0.0007127
SENP3-EIF4A1 3.910008 2.840661 45.47944 0.0001101 0.0048017
SUCNR1 3.918909 6.828456 151.63876 0.0000009 0.0008217
HLF 3.969301 2.010502 61.39614 0.0001951 0.0069235
BAAT 3.986116 1.875604 82.83832 0.0005595 0.0118432
ISG15 3.987277 8.765821 28.31308 0.0005807 0.0120834
HSPA6 4.021950 5.075571 57.94640 0.0000449 0.0030492
ISG20 4.034635 3.041143 30.04930 0.0004749 0.0110002
IFIT2 4.073136 5.933346 24.85427 0.0008941 0.0154317
IFI44 4.086988 4.919038 28.00651 0.0006023 0.0123602
NR4A1 4.159769 6.218755 192.68473 0.0000003 0.0007000
CD68 4.171354 3.317853 34.80694 0.0002861 0.0084898
DHX58 4.190837 2.712811 16.60052 0.0031338 0.0324848
HIVEP2 4.198906 6.659401 48.31647 0.0000882 0.0042472
NT5E 4.316077 7.310700 108.33623 0.0000040 0.0012869
C7orf61 4.365896 2.734189 77.09207 0.0000151 0.0019319
NR4A2 4.367729 3.981776 191.45573 0.0000003 0.0007000
FERMT3 4.484359 2.883749 103.27124 0.0000046 0.0012883
IRF7 4.489884 5.679134 62.13961 0.0000345 0.0028119
TGIF2-RAB5IF 4.494917 4.362682 190.74201 0.0000003 0.0007000
GDF15 4.512745 6.839520 173.03468 0.0000005 0.0007127
CD200R1 4.523281 2.018138 70.30699 0.0000674 0.0037157
GREM1 4.546835 6.032808 90.62883 0.0000080 0.0015101
NUAK2 4.662422 5.571280 189.51363 0.0000003 0.0007000
PTAFR 4.698314 2.295618 58.87163 0.0000423 0.0030190
HAS2 4.774514 5.249723 98.86211 0.0000057 0.0014052
GALNT15 4.843532 3.923216 119.59236 0.0000027 0.0012769
SPDYA 4.964848 3.560782 187.05871 0.0000004 0.0007000
CXCL1 4.990861 2.433813 130.67746 0.0000016 0.0010207
OSM 5.000936 2.248774 46.25914 0.0001035 0.0046794
TNFAIP3 5.158030 8.324103 97.05961 0.0000061 0.0014197
MRC1 5.160553 3.048629 175.47488 0.0000005 0.0007127
MX2 5.179423 4.265989 16.50202 0.0031890 0.0328799
CCL7 5.291829 4.389444 162.54788 0.0000007 0.0007268
IL1B 5.353070 2.593641 121.05582 0.0000021 0.0011397
IFIT3 5.363579 6.476869 32.11417 0.0003783 0.0097807
RSAD2 5.381729 4.795030 15.69902 0.0036876 0.0358349
CXCL2 5.393316 4.112167 241.10541 0.0000001 0.0007000
CA9 5.446761 3.354625 105.39236 0.0000044 0.0012883
IFNB1 5.579821 2.416278 14.13598 0.0049686 0.0431032
CMPK2 5.739321 4.968540 18.36468 0.0023186 0.0270494
IFI44L 5.886140 5.480482 29.97991 0.0004786 0.0110238
OAS3 6.040390 5.476378 55.45416 0.0000530 0.0032675
ANGPTL4 6.667607 7.693979 263.86127 0.0000001 0.0007000
MX1 6.839104 8.213029 71.14538 0.0000206 0.0022828
OAS1 6.914038 6.380700 55.83812 0.0000516 0.0032300
OAS2 7.149848 5.743360 38.37334 0.0002029 0.0070229
PTGS2 7.172085 7.222030 227.27911 0.0000002 0.0007000
IL11 7.811430 5.185583 285.28029 0.0000001 0.0007000

[2]

Non-thresholded Gene Set Enrichment Analysis

Conduct non-thresholded gene set enrichment analysis using the ranked set of genes from Assignment #2.

1.What method did you use? What genesets did you use? Make sure to specify versions and cite your methods.

I used GSEA4.2.3 in this part; Cytoscape 3.9.1, its Enrichment Map application and AutoAnnotation (1.3.5) application for the downstream analysis. [4]

2.Summarize your enrichment results.

knitr::kable(ranked_gene_list_na_pos_versus_na_neg_1648855165869, caption = 'Table 2. Ranked Gene List Virus vs. Mock')
Table 2. Ranked Gene List Virus vs. Mock
NAME SCORE
IL11 7.811430
PTGS2 7.172085
OAS2 7.149848
OAS1 6.914038
MX1 6.839104
ANGPTL4 6.667607
OAS3 6.040390
IFI44L 5.886140
CMPK2 5.739321
IFNB1 5.579821
CA9 5.446761
CXCL2 5.393316
RSAD2 5.381730
IFIT3 5.363579
IL1B 5.353070
CCL7 5.291829
MX2 5.179423
MRC1 5.160553
TNFAIP3 5.158030
OSM 5.000936
CXCL1 4.990861
SPDYA 4.964848
GALNT15 4.843532
HAS2 4.774514
PTAFR 4.698314
NUAK2 4.662423
GREM1 4.546835
CD200R1 4.523281
GDF15 4.512745
TGIF2-RAB5IF 4.494917
IRF7 4.489884
FERMT3 4.484359
NR4A2 4.367728
C7orf61 4.365896
NT5E 4.316078
HIVEP2 4.198906
DHX58 4.190837
CD68 4.171354
NR4A1 4.159769
IFI44 4.086988
IFIT2 4.073136
ISG20 4.034635
HSPA6 4.021950
ISG15 3.987277
BAAT 3.986116
HLF 3.969301
SUCNR1 3.918909
SENP3-EIF4A1 3.910008
ZC3H12A 3.904393
NR4A1AS 3.850720
HAS1 3.840127
CXCL3 3.824323
SPOCD1 3.815799
TNC 3.811428
FOSB 3.811074
ACTBL2 3.808624
CXCL8 3.764355
NXPE2 3.755393
SAA1 3.753236
NR4A3 3.746540
BIRC3 3.746385
SRGN 3.730504
GAL3ST1 3.711185
IFI27 3.706511
APCDD1L 3.695406
STC1 3.653529
IRF8 3.652257
SAMD9 3.629801
SLC12A8 3.620080
LINC01823 3.619946
ZBTB2 3.600436
MICB 3.587570
SLC2A5 3.566019
SERPINE1 3.556188
NFATC2 3.555795
PTX3 3.554543
USP18 3.526600
ANKRD33B 3.521136
SNAI1 3.501171
PCDH15 3.477425
CXCR1 3.476321
MYRFL 3.473980
NPC1L1 3.472580
GIPC3 3.444105
MLKL 3.442330
CDK5R1 3.428745
BST2 3.420476
NFKBIA 3.417202
ANKS4B 3.408031
PLAUR 3.405416
PTPRN 3.400174
TRIM14 3.388913
MAFF 3.370586
IFITM1 3.349915
NR1D1 3.343418
SIX4 3.320190
CDH16 3.290525
MYCT1 3.289963
DDX58 3.283058
MAP3K8 3.271886
IFIH1 3.261873
HELZ2 3.260663
CYP1B1 3.250809
IFI6 3.245873
CFAP43 3.236729
CDCP1 3.221546
LIF 3.218332
CSRNP1 3.209090
TNFSF4 3.194547
NPIPB9 3.187425
SUSD3 3.177775
PER2 3.177066
CD83 3.173820
NFKBIZ 3.159083
PARP10 3.156709
NBPF10 3.123370
CDC42EP2 3.119416
IDI2-AS1 3.112656
PLA2G4A 3.110495
KCNJ6 3.107220
PAPPA 3.106189
SLC25A25 3.094355
MYO10 3.075920
NFKB2 3.074822
IL12A 3.074159
GFPT2 3.053507
SAMHD1 3.052257
TFPI2 3.045211
PCDH8 3.023577
SH2B3 3.016999
TAF4B 3.014949
RELB 3.007213
FNDC11 3.003023
EGR2 2.997124
PFKFB4 2.996145
ADM5 2.995367
APLN 2.991301
TMEM255B 2.982863
IL6 2.982850
NPIPB6 2.977480
TLR4 2.977475
TNFRSF6B 2.973553
LINC01119 2.971468
OSMR 2.968027
SLC20A1 2.959516
ZSWIM4 2.947280
AGTR1 2.936738
ADCY10 2.934266
GCH1 2.930393
FOS 2.924209
TMEM119 2.916719
IPMK 2.909372
TMEM158 2.907376
IFIT1 2.897333
FAM83G 2.890823
PPP1R15A 2.888216
PTGS1 2.871569
ATP10A 2.857127
SAMD9L 2.854908
H2BC6 2.848198
ANXA10 2.847749
ICAM1 2.844774
LOX 2.837510
ATF3 2.834750
HAP1 2.828557
GPR87 2.819893
SLC5A3 2.807390
CDC14A 2.798065
ARRDC3 2.797668
APOL3 2.797154
KCNG1 2.794918
TMEM200A 2.789991
FOSL1 2.786567
PER1 2.773211
SPHK1 2.772888
RFLNA 2.764764
GALNT12 2.762916
ARHGEF28 2.759261
CCNL1 2.752683
RBM47 2.744715
JUNB 2.744661
IP6K3 2.727148
PTGES 2.722689
BHLHE41 2.722265
PRR5L 2.722209
PLOD2 2.720926
SLC19A2 2.718296
H2BC18 2.711889
CPA4 2.708803
ZBTB21 2.703003
INHBE 2.700693
ADGRE5 2.699674
CHD2 2.697284
CCL2 2.692769
BMP6 2.691649
TM4SF1 2.691544
WNK4 2.682955
GABRR2 2.682761
SERPINB2 2.677729
SP100 2.676217
SELPLG 2.668810
KCNN1 2.667134
ITGA5 2.665103
PDCD1LG2 2.657190
SBNO2 2.656249
SGK1 2.647606
H2BC8 2.643823
PARP14 2.642709
TMED7-TICAM2 2.639298
PMAIP1 2.637589
HOXA5 2.628181
TNFRSF10D 2.620613
BMPR1B 2.619521
GRB7 2.610120
TNFSF9 2.605547
IL1R1 2.605356
HERC6 2.604753
CD101 2.589927
F2RL1 2.589487
ADIRF-AS1 2.579662
CSF1 2.579402
STC2 2.574370
APOL6 2.571367
SPINT1 2.569089
OVGP1 2.567849
PHLDA2 2.549979
CPM 2.545456
VEGFC 2.535167
UGCG 2.518274
KLF10 2.515128
TRAF1 2.514945
LOXL3 2.511423
FNIP2 2.511309
SLC2A3 2.509515
TIGD3 2.508575
MEDAG 2.503234
EDEM1 2.498534
BHLHE40 2.496503
KLF5 2.485018
IL15RA 2.483720
PTGER4 2.483473
KLF4 2.478537
PDE10A 2.477695
CA12 2.469995
SLCO2A1 2.466396
DUSP4 2.462814
SOX17 2.458071
NEFM 2.456494
MAPK13 2.450262
HIVEP1 2.437602
LOXL2 2.435605
NBPF19 2.433163
INSYN2B 2.430209
BCL6 2.422277
PARP9 2.414755
MYO3A 2.414730
NR6A1 2.414602
TET3 2.410728
CXCL6 2.410656
TNFRSF1B 2.408509
TG 2.407485
TPBG 2.407003
HLA-E 2.405630
CREBRF 2.394751
CIART 2.392362
RGS4 2.388592
FRMD6 2.387872
MALL 2.383326
INHBA 2.383219
IRF1 2.379943
APOL1 2.379876
ADAM32 2.376574
AMIGO2 2.368723
LSMEM1 2.361432
MCTP2 2.360615
JUN 2.358727
ULBP2 2.358103
BCAR3 2.356021
BCL3 2.352478
ELF3 2.340596
CD44 2.340378
INTS6 2.335218
TRIM38 2.333957
IRAK2 2.332145
SLC22A3 2.328724
SLC43A3 2.324096
EPHA2 2.323694
PDK4 2.321624
TAP1 2.318335
SLC2A9 2.313958
SULF1 2.309025
HTR7 2.306583
ALDH1A3 2.304578
CFB 2.294208
TRIM25 2.294127
DUSP1 2.292234
SERPINB8 2.291079
BRPF1 2.289519
GPR176 2.287500
DDIT3 2.282792
ITGA4 2.280581
RBM15 2.273480
HES1 2.272304
STEAP1 2.269506
SPRED1 2.268266
SLC7A5 2.268056
ARSI 2.258777
RASGRF2 2.257768
DRAM1 2.255817
ETV4 2.255293
DUSP6 2.247526
TNFAIP2 2.246920
DTX3L 2.238600
SMOX 2.238389
FOXN2 2.235189
SPRED3 2.232555
MFAP3L 2.230693
CLK4 2.230614
SNAPC1 2.224079
GPBP1 2.221672
WAKMAR2 2.221539
CACTIN 2.216597
SMURF1 2.206765
ATP8B1 2.201638
IL1RL1 2.200511
TBC1D2 2.199856
NEDD9 2.198391
ACHE 2.184266
PTGIS 2.183773
LRRC8E 2.181391
SEL1L3 2.178554
KCNAB1 2.174609
HFE 2.173138
SEC24A 2.171192
NFKBID 2.170539
GADD45B 2.169566
CHD1 2.167425
ZBTB10 2.166943
HS6ST2 2.158807
EIF2AK2 2.155542
LDB2 2.155333
STARD13 2.146103
GBP3 2.142594
TYMP 2.142315
THY1 2.139841
NBPF26 2.135125
RXFP1 2.133374
TENT5C 2.132303
IL33 2.129479
THSD1 2.128001
ARHGAP20 2.123484
SLC38A5 2.122949
NRG3 2.120995
KLF11 2.114600
ERRFI1 2.113944
MVP 2.111094
C1QTNF1 2.109298
DPP4 2.104114
TMEM87B 2.099924
PDE7A 2.096324
IFRD1 2.095692
ZNF317 2.095386
UBASH3B 2.093595
NBPF14 2.093447
HOXA-AS2 2.088457
CDH6 2.086026
SH3RF1 2.084813
FGF7 2.083364
SQSTM1 2.082316
KLF9 2.079559
ADCY7 2.076348
RGS16 2.075771
CLCF1 2.075358
NPIPB15 2.073422
RAPGEF2 2.072268
PCSK9 2.069441
SKIL 2.067251
DOK5 2.067119
ITGA2 2.062052
ZNF844 2.061578
PDZD2 2.058617
TRIM22 2.055730
PFKFB3 2.054620
BAIAP2L1 2.054319
ADM2 2.052314
DBP 2.048629
PIK3CD 2.048266
HAPLN3 2.047483
EMP1 2.044095
LIPG 2.043150
H2BC5 2.042077
EVC2 2.040074
HRH1 2.039099
EGR1 2.037634
TLE1 2.036129
KCNE4 2.032976
CASP4 2.031420
ARRDC2 2.028687
PIGA 2.025300
RSRC2 2.024864
PIM3 2.022238
GTF2IRD1 2.022119
LRIG3 2.022030
MYD88 2.019954
ERO1A 2.009337
RLF 2.009219
TGFBI 2.008175
PTBP3 2.004432
ACOT13 -2.000114
PLK1 -2.000453
CPVL -2.005104
FANCL -2.006840
CHURC1-FNTB -2.009534
UQCR10 -2.010785
HADH -2.010848
SVIP -2.011910
PPP1R3C -2.018053
IL17B -2.019427
CHCHD5 -2.019536
ATP5MPL -2.020557
TIMM8B -2.021806
MYL3 -2.022303
ATP5MC1 -2.023177
GSTM4 -2.024015
DHRS11 -2.024969
GJA5 -2.025338
SKA3 -2.028284
ETFRF1 -2.029499
PIFO -2.030697
DNAJC15 -2.036522
RDH5 -2.037272
SMDT1 -2.037491
PET100 -2.043188
HACD1 -2.043966
ERH -2.046144
NIFK-AS1 -2.046841
PPP1R14C -2.047443
ATP5MF -2.049363
NEXN -2.052929
INKA2-AS1 -2.054012
NSMCE4A -2.054613
ST7-AS1 -2.056492
MMP15 -2.056655
ABHD11 -2.056984
PLCXD3 -2.058581
FAM20A -2.059499
MYLK -2.060309
COX8A -2.061003
ACYP1 -2.061078
NDUFC1 -2.062849
DGCR6 -2.064497
SH3RF2 -2.067586
TMEM144 -2.068687
PARP1 -2.069997
ATP5PD -2.070352
ICA1 -2.073635
HIGD2A -2.075338
CDCA7 -2.075812
FAM229B -2.080910
PLPP7 -2.082147
PHACTR1 -2.086106
DOK7 -2.086878
GNG7 -2.087833
EMP2 -2.088005
ASB2 -2.088868
GTSE1 -2.089318
EFCAB7 -2.091420
KLHL3 -2.095120
CDKN2C -2.096007
MYBPC3 -2.098119
GUCY1A1 -2.098464
ATP5MC3 -2.098677
IL20RA -2.099056
NAP1L3 -2.099201
MRPL53 -2.101326
ANAPC16 -2.104280
MGST3 -2.109753
BEX2 -2.111248
ITM2A -2.118308
CMC4 -2.118674
NDUFB2 -2.118844
UQCRQ -2.122164
SYNM -2.122636
ATP5ME -2.123243
SHCBP1 -2.129380
HMGN5 -2.130325
GLIDR -2.130896
DECR1 -2.132020
PRC1 -2.133292
SLC5A1 -2.133719
TMEM97 -2.134051
DES -2.134094
DLGAP1-AS1 -2.134387
ULK4 -2.138354
LINC02762 -2.143704
LINC01351 -2.148929
MTURN -2.152774
PMEL -2.153426
MDP1 -2.154549
ADCY5 -2.158902
NDUFS6 -2.162245
USH1C -2.162887
INKA2 -2.162963
DNAJC28 -2.164137
TAFA2 -2.164442
MPC1 -2.165892
PCBD1 -2.167003
HAND2-AS1 -2.167011
PLN -2.167092
ROGDI -2.167942
MYL9 -2.170793
HMGN2 -2.174406
C10orf71 -2.176344
LINC00880 -2.177140
HMGCLL1 -2.178475
RBMS3-AS3 -2.180075
DAND5 -2.181967
SSPN -2.183134
REXO5 -2.195596
COX6C -2.195835
LINC00526 -2.197931
SELENOW -2.198793
ACADSB -2.198825
CDC20 -2.200800
VSNL1 -2.201836
ACAT1 -2.204879
GON7 -2.209077
KCNQ2 -2.214763
CDC6 -2.216078
SYNJ2BP-COX16 -2.221443
PLK4 -2.221475
SLC2A8 -2.222631
SCHIP1 -2.222649
TBX20 -2.225745
LYPD6 -2.228899
YPEL1 -2.232118
KIF22 -2.232446
ANKRD1 -2.238789
CTF1 -2.240603
UNC45B -2.241744
BCL2A1 -2.242443
SRP14-AS1 -2.245190
LYRM9 -2.250067
NIPSNAP3B -2.253375
BANCR -2.253846
DERL3 -2.255450
HAND2 -2.255680
ACOT1 -2.259996
TECRL -2.264283
CAMK2A -2.271184
CRIP2 -2.272728
COX7B -2.281664
KIAA0319 -2.281730
HAND1 -2.281999
S100A6 -2.287949
CORO6 -2.289831
BIK -2.292042
CCND2-AS1 -2.295584
BOLA1 -2.296717
NDUFA3 -2.302154
ACSM5 -2.303018
DRD1 -2.305130
COL21A1 -2.309664
ATP5PF -2.312218
GP1BB -2.314509
MORN2 -2.319151
TK1 -2.320188
CDCA5 -2.322462
LRRC52-AS1 -2.324422
LINC01778 -2.327603
FPGT -2.329109
TMOD1 -2.329743
CLIC5 -2.332800
PDE6B -2.333192
C17orf97 -2.335326
FOXM1 -2.340321
TRDN-AS1 -2.340616
CRYAB -2.344243
HSD17B8 -2.345639
DNAAF3 -2.348180
UBE2C -2.349332
TAGLN3 -2.354777
ZSCAN16-AS1 -2.356235
MRPS28 -2.358498
FN3K -2.364778
RPA3 -2.365246
NTF4 -2.377098
VIPR1 -2.382483
EPHX2 -2.384289
HSPB1 -2.385072
C14orf180 -2.386624
RCSD1 -2.389719
C11orf74 -2.390511
SLC30A3 -2.395008
PHYHD1 -2.395036
CENPH -2.395726
SLC8A1 -2.406968
TRAPPC6A -2.409063
NES -2.412128
NEBL -2.413640
TMEM141 -2.417552
LRRC10 -2.418899
NUSAP1 -2.423946
GSG1 -2.424480
KCNS2 -2.425896
PHOSPHO2 -2.427787
EXOC3-AS1 -2.430176
LINC02384 -2.433270
IDNK -2.433926
LRRCC1 -2.437214
SFRP2 -2.438680
CLYBL -2.443257
DUSP27 -2.443680
TSTD1 -2.443933
HJURP -2.451450
MTERF2 -2.454024
ACOT2 -2.463990
PRADC1 -2.464355
PHACTR3 -2.466546
RPE65 -2.467311
ADHFE1 -2.470553
ZNF793-AS1 -2.482754
APOBEC2 -2.495307
CCNB2 -2.500282
GIHCG -2.502606
SMIM5 -2.507403
UPK1B -2.518697
C11orf1 -2.523570
CDK1 -2.528634
MINCR -2.531948
PNMT -2.532905
CKAP2L -2.533517
DEPDC1 -2.538446
COX7C -2.538748
FERMT1 -2.540029
RMI2 -2.542336
TYMSOS -2.551361
NEK2 -2.561090
SLC26A9 -2.565358
CRABP2 -2.565913
MIR1-1HG-AS1 -2.567849
PKIA -2.570428
ALDOC -2.573856
PKMYT1 -2.575518
GPR183 -2.580100
SFRP5 -2.580538
RRM2 -2.581340
BRINP2 -2.587693
TMEM163 -2.592041
BIRC5 -2.603424
CASQ1 -2.614019
NDUFB1 -2.617046
C11orf71 -2.622072
TMEM71 -2.625232
MLIP -2.626909
TYRP1 -2.631008
UBE2E1 -2.633303
PDE1A -2.636327
SLC27A6 -2.640879
DTL -2.641167
SGCA -2.644098
GPX3 -2.652738
MYZAP -2.654654
PLAC1 -2.658369
CASQ2 -2.660241
CAVIN3 -2.661827
ANLN -2.662587
SPHKAP -2.668391
IGSF5 -2.672417
SYNPO2L -2.672782
GPR22 -2.683250
SMYD1 -2.687409
SORCS3 -2.687721
LINC00881 -2.692807
HRH2 -2.694184
PEBP4 -2.695043
CDCA8 -2.698342
CEP55 -2.708550
SPX -2.708569
AMT -2.719618
DIRAS3 -2.722534
CDC45 -2.726066
POLE2 -2.734335
TRDN -2.737878
NMRK2 -2.747681
PIMREG -2.749342
EPN3 -2.749571
FPGT-TNNI3K -2.753526
REC114 -2.761811
SH3BGR -2.764689
MOG -2.766072
CSPG5 -2.786076
H4C3 -2.794520
SMIM1 -2.796013
SRPK3 -2.800608
SLC15A2 -2.804699
SLC38A3 -2.806756
ASF1B -2.817701
TNNT2 -2.820532
RAB9B -2.823723
EMC10 -2.824767
IMMP1L -2.829254
HMGB2 -2.830279
FMC1 -2.830632
LINC01456 -2.832458
NCAPH -2.854564
ENPP5 -2.856968
KIF2C -2.860460
CRIP1 -2.865284
VSTM2L -2.866543
LGALS3 -2.871758
LEFTY2 -2.880727
CSRP3 -2.882775
C11orf52 -2.904686
MCM5 -2.908502
NREP -2.911058
RXRG -2.913305
UBE2T -2.922022
HRC -2.948080
NEIL3 -2.948272
SGO1 -2.953492
PTGES3L -2.953571
AQP10 -2.967106
LINC01405 -2.969873
G0S2 -2.979050
FRMD3 -2.990653
TOP2A -3.004569
HOPX -3.009609
C1orf105 -3.013779
NUDT7 -3.015060
PANCR -3.015240
COL9A1 -3.024658
SPC24 -3.025167
ZWINT -3.030731
BBOX1-AS1 -3.034916
DHFR -3.035134
CRYM -3.048275
SELENOP -3.060758
KIF20A -3.066232
CAV3 -3.066379
GABRA4 -3.068427
CDCA3 -3.086259
NPPA -3.091703
SLC5A12 -3.096242
FGF13-AS1 -3.097264
PPP1R1C -3.100553
ITGB1BP2 -3.103756
AIF1L -3.108962
PLCB2 -3.129927
CALN1 -3.145096
TESC -3.150083
NUF2 -3.151356
SPSB4 -3.155675
LSMEM2 -3.164595
PPP1R1A -3.171572
KLHDC9 -3.218902
DMAC1 -3.234254
FAM133A -3.237091
CHCHD10 -3.261912
NDC80 -3.269491
FSD2 -3.274605
OIP5 -3.282617
FITM1 -3.291142
TRIM54 -3.298866
CENPU -3.303800
CDKN3 -3.334427
AURKB -3.351708
ATP6V1G2 -3.357918
DLGAP5 -3.375682
GPD1 -3.377976
SMPX -3.395799
LMOD2 -3.403714
HSPB3 -3.409678
MYH7 -3.415903
C1QL1 -3.445765
TNNI3 -3.479622
FABP3 -3.492141
MARCHF11 -3.530975
MB -3.542870
CD36 -3.544471
SLC35D3 -3.553160
LINC01182 -3.561014
LDHD -3.576655
LINC01611 -3.581984
MIR133A1HG -3.586468
ACTC1 -3.599775
MYLK-AS1 -3.614126
PCLAF -3.618731
GINS2 -3.632645
LDB3 -3.633489
GJD2 -3.648797
TNNI1 -3.649594
NAV2-AS2 -3.659571
SUSD2 -3.664531
RAD51AP1 -3.668636
CORIN -3.695186
CPNE5 -3.696150
HSPB7 -3.772049
NME5 -3.772923
MYL4 -3.789321
ACE2 -3.792261
FGF12 -3.795245
TROAP -3.795809
CCDC34 -3.807975
CKMT2 -3.843017
ODAM -3.875695
MYL7 -3.935387
ADPRHL1 -3.938632
S100A8 -3.987699
MAOB -4.013483
TNMD -4.017589
TMSB15A -4.023837
MSS51 -4.049343
CENPM -4.064744
TCAP -4.067439
PBK -4.114213
COX6A2 -4.168300
IRX4-AS1 -4.282455
TNNC1 -4.285373
LINC02502 -4.298163
FAM111B -4.336571
SPC25 -4.366327
FXYD1 -4.430059
ACTA1 -4.549569
HHATL -4.724839
METTL7B -4.984910
ALAS2 -5.044219
FBXL22 -5.289780
MYL2 -5.499683
KCNIP2 -5.719563
PGAM2 -5.823109

[2]

  • 16035 gene sets with size larger than 200 or smaller than 15 were filtered out from a total of 16746, the remaining 711 gene sets were used in this analysis. We used a stricter boundary to obtain more rigorous results. We selected the permutation number of 1000, which has a suitable running time for the program.

  • The Positive Phenotype (na_pos):

Table 3. Enrichment Plot of the Top 20 Gene Sets Ranked in the Positive(Virus) Phenotype

517 out of 711 gene sets are returned in the Virus (na_pos) sub-type. 421 gene sets are significant at FDR < 25%. 304 gene sets are significantly enriched at nominal p-value < 1%. 366 gene sets are significantly enriched at nominal p-value < 5%. The most related gene set in this sub-type according to the analysis is DEFENSE RESPONSE GOBP GO:0006952, with an enrichment score (ES) of 0.5994537 and a normalized enrichment score (NES) of 4.323445.

Figure 1. Profile of the Running ES Score & Positions of DEFENSE RESPONSE GOBP GO:0006952 on the Rank Ordered List

Figure 2. Random ES Distribution of DEFENSE RESPONSE GOBP GO:0006952

knitr::kable(DEFENSE_RESPONSE_GOBP, caption = 'Table 4. DEFENSE RESPONSE GOBP')
Table 4. DEFENSE RESPONSE GOBP
NAME RANK.IN.GENE.LIST RANK.METRIC.SCORE RUNNING.ES CORE.ENRICHMENT
OAS2 2 7.149848 0.0245612 Yes
OAS1 3 6.914038 0.0508740 Yes
MX1 4 6.839104 0.0769017 Yes
OAS3 6 6.040390 0.0985651 Yes
IFI44L 7 5.886140 0.1209661 Yes
IFNB1 9 5.579821 0.1408767 Yes
CXCL2 11 5.393316 0.1600776 Yes
RSAD2 12 5.381730 0.1805589 Yes
IFIT3 13 5.363579 0.2009711 Yes
IL1B 14 5.353070 0.2213434 Yes
CCL7 15 5.291829 0.2414825 Yes
MX2 16 5.179423 0.2611939 Yes
CXCL1 20 4.990861 0.2762141 Yes
PTAFR 24 4.698314 0.2901210 Yes
IRF7 30 4.489884 0.3005857 Yes
IFIT2 40 4.073136 0.3041663 Yes
ISG20 41 4.034635 0.3195210 Yes
ISG15 43 3.987277 0.3333709 Yes
CXCL3 51 3.824323 0.3386536 Yes
CXCL8 56 3.764355 0.3476816 Yes
SAA1 58 3.753236 0.3606409 Yes
IRF8 66 3.652257 0.3652688 Yes
MICB 71 3.587570 0.3736240 Yes
SERPINE1 73 3.556188 0.3858333 Yes
PTX3 75 3.554543 0.3980364 Yes
CXCR1 80 3.476321 0.4059682 Yes
BST2 86 3.420476 0.4123630 Yes
TRIM14 91 3.388913 0.4199622 Yes
IFITM1 93 3.349915 0.4313865 Yes
DDX58 98 3.283058 0.4385829 Yes
IFIH1 100 3.261873 0.4496721 Yes
IFI6 103 3.245873 0.4593759 Yes
TNFSF4 108 3.194547 0.4662354 Yes
CD83 112 3.173820 0.4743406 Yes
NFKB2 123 3.074822 0.4727974 Yes
IL12A 124 3.074159 0.4844968 Yes
SAMHD1 126 3.052257 0.4947883 Yes
RELB 131 3.007213 0.5009348 Yes
IL6 138 2.982850 0.5043396 Yes
TLR4 140 2.977475 0.5143465 Yes
TNFRSF6B 141 2.973553 0.5256630 Yes
GCH1 148 2.930393 0.5288683 Yes
FOS 149 2.924209 0.5399969 Yes
IFIT1 153 2.897333 0.5470498 Yes
ICAM1 161 2.844774 0.5486047 Yes
APOL3 169 2.797154 0.5499783 Yes
FOSL1 172 2.786567 0.5579342 Yes
ADGRE5 191 2.699674 0.5443672 Yes
CCL2 193 2.692769 0.5532907 Yes
SP100 199 2.676217 0.5568531 Yes
PMAIP1 209 2.637589 0.5549704 Yes
TNFRSF10D 211 2.620613 0.5636192 Yes
F2RL1 218 2.589487 0.5655270 Yes
LOXL3 231 2.511423 0.5591907 Yes
CXCL6 258 2.410656 0.5339279 Yes
TNFRSF1B 259 2.408509 0.5430939 Yes
HLA-E 262 2.405630 0.5496001 Yes
INHBA 268 2.383219 0.5520474 Yes
IRF1 269 2.379943 0.5611048 Yes
APOL1 270 2.379876 0.5701619 Yes
ULBP2 276 2.358103 0.5725136 Yes
ELF3 279 2.340596 0.5787722 Yes
CD44 280 2.340378 0.5876790 Yes
TRIM38 282 2.333957 0.5952369 Yes
CFB 293 2.294208 0.5907229 Yes
TRIM25 294 2.294127 0.5994537 Yes
TRIM22 381 2.055730 0.4933699 No
PIK3CD 386 2.048266 0.4958670 No
HRH1 392 2.039099 0.4970047 No
EGR1 393 2.037634 0.5047594 No
MYD88 403 2.019954 0.5005262 No
CAMK2A 549 -2.271184 0.3171166 No
EPHX2 588 -2.384289 0.2758595 No
HMGB2 702 -2.830279 0.1369618 No
ODAM 805 -3.875695 0.0166122 No
S100A8 808 -3.987699 0.0291392 No
  • The Negative Phenotype (na_neg):

Table 5. Enrichment Plot of the Top 20 Gene Sets Ranked in the negative(Mock) Phenotype

194 out of 711 gene sets are returned in the Mock (na_neg) sub-type. 98 gene sets of them are significantly enriched at FDR < 25%. 69 gene sets of them are significantly enriched at nominal p-value < 1%. 89 gene sets of them are significantly enriched at nominal p-value < 5%. The most related gene set in this sub-type according to the analysis is CELL CYCLE REACTOME R-HSA-1640170.1, with an enrichment score (ES) of -0.56024605 and a normalized enrichment score (NES) of -3.6521144.

Figure 3. Profile of the Running ES Score & Positions of CELL CYCLE REACTOME R-HSA-1640170.1 on the Rank Ordered List

Figure 4. Random ES Distribution of CELL CYCLE REACTOME R-HSA-1640170.1

knitr::kable(CELL_CYCLE_REACTOME, caption = 'Table 6. CELL CYCLE REACTOME')
Table 6. CELL CYCLE REACTOME
NAME RANK.IN.GENE.LIST RANK.METRIC.SCORE RUNNING.ES CORE.ENRICHMENT
CDC14A 167 2.798065 -0.1873640 No
PLK1 409 -2.000453 -0.4754434 No
GTSE1 465 -2.089318 -0.5270098 No
CDKN2C 468 -2.096007 -0.5113444 No
ANAPC16 475 -2.104280 -0.5006769 No
CDC20 523 -2.200800 -0.5411358 Yes
CDC6 528 -2.216078 -0.5269628 Yes
PLK4 530 -2.221475 -0.5089405 Yes
TK1 566 -2.320188 -0.5331537 Yes
CDCA5 567 -2.322462 -0.5129871 Yes
FOXM1 575 -2.340321 -0.5015374 Yes
UBE2C 580 -2.349332 -0.4862072 Yes
RPA3 585 -2.365246 -0.4707388 Yes
CENPH 595 -2.395726 -0.4613429 Yes
HJURP 614 -2.451450 -0.4628700 Yes
CCNB2 623 -2.500282 -0.4512988 Yes
CDK1 628 -2.528634 -0.4344116 Yes
RMI2 635 -2.542336 -0.4199404 Yes
NEK2 637 -2.561090 -0.3989692 Yes
PKMYT1 643 -2.575518 -0.3829424 Yes
RRM2 646 -2.581340 -0.3630628 Yes
BIRC5 649 -2.603424 -0.3429914 Yes
UBE2E1 656 -2.633303 -0.3277302 Yes
CDCA8 676 -2.698342 -0.3283809 Yes
CDC45 681 -2.726066 -0.3097794 Yes
POLE2 682 -2.734335 -0.2860364 Yes
NCAPH 705 -2.854564 -0.2891329 Yes
KIF2C 707 -2.860460 -0.2655621 Yes
MCM5 714 -2.908502 -0.2479114 Yes
TOP2A 726 -3.004569 -0.2357636 Yes
SPC24 732 -3.025167 -0.2158324 Yes
ZWINT 733 -3.030731 -0.1895157 Yes
DHFR 735 -3.035134 -0.1644282 Yes
KIF20A 738 -3.066232 -0.1403381 Yes
NUF2 751 -3.151356 -0.1281831 Yes
NDC80 759 -3.269491 -0.1086652 Yes
OIP5 761 -3.282617 -0.0814288 Yes
CENPU 764 -3.303800 -0.0552758 Yes
AURKB 766 -3.351708 -0.0274395 Yes
GINS2 788 -3.632645 -0.0225122 Yes
CENPM 813 -4.064744 -0.0176351 Yes
SPC25 821 -4.366327 0.0114069 Yes
  • However, this sample contains only 831 objects, which might be too few for the GSEA analysis.

[4]

3.How do these results compare to the results from the thresholded analysis in Assignment #2. Compare qualitatively. Is this a straight forward comparison? Why or why not?

These results do not have a threshold which is a cut-off according to p-value, so the returned gene sets are slightly different. It is a straightforward comparison. Because they are both imported from the same normalized data.

Visualize your Gene set Enrichment Analysis in Cytoscape

Visualizing the results from the non-thresholded gene set enrichment analysis in Cytoscape by Using Enrichment Map and AutoAnnotate.

1. Create an enrichment map - how many nodes and how many edges in the resulting map? What thresholds were used to create this map? Make sure to record all thresholds. Include a screenshot of your network prior to manual layout.

  • In the Virus vs Mock gene set enrichment map visualization, we used FDR q-value of 0.01, p-value of 0.1 and edge similarity value of 0.375 as cutoff. We selected all NES. The Metric was set to 50% Jaccard combined with 50% Overlap. There are 339 nodes and 3033 edges in this visualized enrichment map.

Figure 5. Pre-Analysis Parameters Used for the GSEA Analysis

  • Below is the over view of the network.

Figure 6. Overview of the Network

2. Annotate your network - what parameters did you use to annotate the network. If you are using the default parameters make sure to list them as well.

  • We used the default settings of the AutoAnnotate application to annotate the entire map, we selected to layout network to prevent the overlap of the clusters. We used GS_DESCR as label column.

Figure 7. Pre-Annotation Parameters

  • We selected a round shape, border width of 3, opacity of 20%, font scale of 20% and minimum font size of 4.

Figure 8. Annotation Parameters

3. Make a publication ready figure - include this figure with proper legends in your notebook.

Figure 9. Mock vs. Virus Enrichment Map. Red: Virus group; blue: Mock group. The virus group coming from in vitro hiPSC-CMs infected with SARS-CoV-2 while the Mock group are in vitro hiPSC-CMs not infected with SARS-CoV-2

4. Collapse your network to a theme network. What are the major themes present in this analysis? Do they fit with the model? Are there any novel pathways or themes?

  • The major themes that fit with the model include blood circulation heart,actin contraction filament, organism organelle organization, mitotic cycle sister, signaling cellular interferon, apoptotic programmed death, naba factor matrisome, positive cell proliferation, response biotic virus, taxis migration chemotaxis, programmed cell death, component movement migration, hallmark allograft rejection, activation involved neutrophil, viral life multi, negative regulation cellular, regulation metabolic positive, inflammation response stress, vasculature development, protein localization transport, transcription regulation biosynthetic, transmembrane transporter activity.

  • There are also novel pathways and themes that do not fit with the model: epithelial mesenchymal, myogenesis, tnfa signaling, inflammatory response, hypoxia, muscel development tissue, extracellular organization matrix, estrogen response, oxidative phosphorylation, e2f targets, p53 pathway, interferon gamma alpha, uv response, kras signaling, g2m checkpoint and il2 stat5.

Figure 10. Mock vs. Virus Collapsed Theme Network

[10]

Interpretation and detailed view of results

1. Do the enrichment results support conclusions or mechanism discussed in the original paper? How do these results differ from the results you got from Assignment #2 thresholded methods

Yes, the enrichment results support conclusions and mechanisms discussed in the original paper at some point.

The original paper concluded that SARS-CoV-2 infection (Virus group) induces significant transcriptional changes within hiPSC-CMs(human iPSC cardiomyocytes in vitro) in gene pathways related to cellular metabolism and immune response.

In the Virus group, considerable amount of gene sets and themes are related to reacting to abnormality according to the positive phenotype enrichment plot (Table 3.) and the enrichment map (Figure 9.), such as virus response, inflammatory response, defense response, mass of apoptosis, etc. There are also many themes related to metabolic, transcriptional and cellular pathways.

But we didn’t see any significant themes about normal heart activities as those shown in the Mock group. So we conclude that the SARS-CoV-2 infection might lead to immune response and affect normal heart activity in metabolic, transcriptional and cellular pathways, such as functional alterations, transcriptional changes, apoptosis mentioned in the result of original paper.

2. Can you find evidence, i.e. publications, to support some of the results that you see. How does this evidence support your result?

  • Yes. Compared to the in vitro experiment conducted by Sharma et al., Kumar et al. performed a study on well-characterized cardiomyocytes from lymphoblastoid cell line (LCL) reprogrammed iPSC lines of 12 participants belong to four sibships. The samples were analyzed by genome-wide RNA sequencing based transcriptomic and functional annotation.

In the enrichment analysis, the CM-upregulated transcriptome showed significantly high enrichment in the gene set GSE150392 (the original data for this assignment) down-regulated by SARS-CoV-2 infection in cardiomyocytes. [11]

Figure S1. Table of Gene Sets From Kumar et, al.

[11]

  • Perez-Bermejo et al. also indicated that SARS-CoV-2 can productively infect human cardiomyocytes inducing broad transcriptional changes, disrupt intracellular features after using iPSC-derived tissues to analyze to evaluate the SARS-CoV-2 infectivity of different heart cell types by using scRNA-sequencing and immunofluorescence.

They observed that SARS-CoV-2 infection creates precise and ordered disruptions to the myofibrillar structure and dissolution of the cardiac contractile machinery, which would lead to cardiac functional collapse. [12]

Add a post analysis to your main network using specific transcription factors, microRNAs or drugs. Include the reason why you chose the specific miRs, TFs or drugs (i.e publications indicating that they might be related to your model). What does this post analysis show?

I will choose Troponin I to study, since the increase of Troponin I is a clinical biomarkers of cardiac damage as well as the strongest predictors of mortality in COVID-19 patients. [12]

Troponin I (TnI) is the protein subunit that inhibits muscle contraction in the absence of calcium. The interaction of troponin I with actin is weakened in the presence of Ca2+. Troponin I then move from actin to a larger distance and the steric blocking of the actin-myosin interaction vanishes. [13]

It is not surprising that the increase of Troponin I lead to cardiac damage, since it is the inhibitor of muscle contraction. It is also possible that the level of Ca2+ could have further impact on the SARS-CoV-2 influenced cardiomyocytes infection and cardiac functional damage, since the inhibition of troponin I on muscle contraction increases when the Ca2+ level decreases. This can be studied in the future.

Reference

1. Sharma A, Garcia Jr G, Wang Y, Plummer JT, Morizono K, Arumugaswami V, et al. Human iPSC-derived cardiomyocytes are susceptible to sars-cov-2 infection. Cell Reports Medicine. 2020;1:100052.

2. Xie Y. Knitr: A comprehensive tool for reproducible research in r. Implement Reprod Res. 2014;1:20.

3. James DA, Falcon S. RSQLite: SQLite interface for r. R package version 011. 2011;1.

4. Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, et al. Pathway enrichment analysis and visualization of omics data using g: Profiler, gsea, cytoscape and enrichmentmap. Nature protocols. 2019;14:482–517.

5. Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: A network-based method for gene-set enrichment visualization and interpretation. PloS one. 2010;5:e13984.

6. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences. 2005;102:15545–50.

7. Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J, et al. PGC-1\(\alpha\)-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nature genetics. 2003;34:267–73.

8. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP. Molecular signatures database (msigdb) 3.0. Bioinformatics. 2011;27:1739–40.

9. Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database hallmark gene set collection. Cell systems. 2015;1:417–25.

10. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13:2498–504.

11. Kumar S, Curran JE, Kumar K, DeLeon E, Leandro AC, Peralta J, et al. Disease modeling and disease gene discovery in cardiomyopathies: A molecular study of induced pluripotent stem cell generated cardiomyocytes. International journal of molecular sciences. 2021;22:3311.

12. Perez-Bermejo JA, Kang S, Rockwood SJ, Simoneau CR, Joy DA, Silva AC, et al. SARS-cov-2 infection of human iPSC–derived cardiac cells reflects cytopathic features in hearts of patients with covid-19. Science translational medicine. 2021;13:eabf7872.

13. Filatov V, Katrukha A, Bulargina T, Gusev N. Troponin: Structure, properties, and mechanism of functioning. Biochemistry c/c of Biokhimiia. 1999;64:969–85.